* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/MGRASTer.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘MGRASTer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MGRASTer’ version ‘0.9’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MGRASTer’ can be installed ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RJSONIO’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/11s] NOTE
.onAttach: no visible global function definition for ‘packageVersion’
.onAttach: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible global function definition for ‘fromJSON’
call.MGRAST: no visible binding for global variable ‘.MGRAST’
call.MGRAST: no visible global function definition for ‘download.file’
call.MGRAST: no visible global function definition for ‘isValidJSON’
call.MGRAST: no visible global function definition for ‘fromJSON’
doc.MGRAST: no visible binding for global variable ‘.MGRAST’
doc.MGRAST: no visible global function definition for ‘str’
load.MGRAST: no visible binding for global variable ‘.MGRAST’
parse.MGRAST: no visible binding for global variable ‘.MGRAST’
this.package: no visible binding for global variable ‘.MGRAST’
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’
 ERROR
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > ##############################################################################
  > #
  > #  Although this package is essentially a wrapper for a distinct API,
  > #  the design is intended to ensure stability with respect to the R platform,
  > #  independent of changes to that API.
  > #
  > #  The MG-RAST API is developed in a dynamic environment.  Our goal here is
  > #  for package functionality to handle well in the face of significant API changes,
  > #  patches, hotfixes, etc.
  > #
  > #  (Of course, this only applies to interim periods between package versions,
  > #  which do regularly incorporate latest API updates.)
  > #
  > #  In particular, these package tests test the package, not the API.  They are 
  > #  written with the thought that the package will still "work" in a formal sense,
  > #  even when the API does not.  This refers to buggy behavior, s as well as 
  > #  occasional server downtime.
  > #
  > #  The effort made to accommodate API updates dynamically is par of this approach, 
  > #  comprised of the build.MGRAST() and load.MGRAST() functions.  They can only 
  > #  provide so much resilience, of course.
  > #
  > #  One of the challenges of this project has been that, although the API
  > #  is formally specified, best results in practice have required experimentation
  > #  and been modeled on examples.
  > #
  > #  Accordingly, these URLs from API documentation form the backbone of testing. 
  > #  Some are also copied to the doc examples of call.MGRAST() and parse.MGRAST().
  > #  Updates here may require updates there.  Last updated April 2014.
  > #
  > #  Per correspondence with CRAN, the policy in these tests is not to actually
  > #  attempt communicaton with the MG-RAST API server.  Such tests are present 
  > #  below in comments, however.
  > #
  > #
  > #  http://api.metagenomics.anl.gov/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt
  > #  http://api.metagenomics.anl.gov/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO
  > #  http://api.metagenomics.anl.gov/compute/alphadiversity/mgm4447943.3?level=order
  > #  http://api.metagenomics.anl.gov/download/mgm4447943.3?file=350.1
  > #  http://api.metagenomics.anl.gov/download/mgm4447943.3?stage=650
  > #  http://api.metagenomics.anl.gov/library?limit=20&order=name
  > #  http://api.metagenomics.anl.gov/library/mgl52924?verbosity=full
  > #  http://api.metagenomics.anl.gov/m5nr/ontology?source=Subsystems&min_level=level3
  > #  http://api.metagenomics.anl.gov/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus
  > #  http://api.metagenomics.anl.gov/m5nr/sources
  > #  http://api.metagenomics.anl.gov/m5nr/accession/YP_003268079.1
  > #  http://api.metagenomics.anl.gov/m5nr/alias/IPR001478
  > #  http://api.metagenomics.anl.gov/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro
  > #  http://api.metagenomics.anl.gov/m5nr/function/sulfatase?source=GenBank
  > #  http://api.metagenomics.anl.gov/m5nr/organism/akkermansia?source=KEGG
  > #  http://api.metagenomics.anl.gov/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL
  > #  http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=family&source=RefSeq&result_type=abundance&evalue=15
  > #  http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=level3&source=Subsystems&result_type=abundance&identity=80&filter_level=phylum&filter=Firmicutes
  > #  http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&source=KEGG&result_type=evalue&length=25
  > #  http://api.metagenomics.anl.gov/metadata/template
  > #  http://api.metagenomics.anl.gov/metadata/cv
  > #  http://api.metagenomics.anl.gov/metadata/export/mgp128
  > #  http://api.metagenomics.anl.gov/metagenome?limit=20&order=name
  > #  http://api.metagenomics.anl.gov/metagenome/mgm4447943.3?verbosity=metadata
  > #  http://api.metagenomics.anl.gov/project?limit=20&order=name
  > #  http://api.metagenomics.anl.gov/project/mgp128?verbosity=full
  > #  http://api.metagenomics.anl.gov/sample?limit=20&order=name
  > #  http://api.metagenomics.anl.gov/sample/mgs25823?verbosity=full
  > #  http://api.metagenomics.anl.gov/validation/template/
  > #  http://api.metagenomics.anl.gov/validation/data/?template=
  > #
  > ##############################################################################
  > 
  > 
  > library(MGRASTer)
  MGRASTer (0.9 02e288)
  > 
  > #-----------------------------------------------------------------------------
  > #  test package environment & local API representation.
  > #  also, test access and slicing of documentation.
  > #  we would like a simpler way to list controlled vocabularies
  > #  than the last two examples, but that must wait.
  > #-----------------------------------------------------------------------------
  > 
  > ls (.MGRAST)
  [1] "API"          "API.version"  "server"       "this.package"
  > get ("server", envir=.MGRAST)
  [1] "http://api.metagenomics.anl.gov"
  > get ("this.package", envir=.MGRAST)
        name 
  "MGRASTer" 
  > get ("API.version", envir=.MGRAST)
  [1] "1"
  > get ("API", envir=.MGRAST)
  $annotation
  $annotation$info
  $annotation$info$parameters
  $annotation$info$parameters$body
  named list()
  
  $annotation$info$parameters$options
  named list()
  
  $annotation$info$parameters$required
  named list()
  
  
  $annotation$info$request
  [1] "http://api.metagenomics.anl.gov/annotation"
  
  $annotation$info$name
  [1] "info"
  
  $annotation$info$type
  [1] "synchronous"
  
  $annotation$info$method
  [1] "GET"
  
  $annotation$info$attributes
  [1] "self"
  
  $annotation$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $annotation$sequence
  $annotation$sequence$request
  [1] "http://api.metagenomics.anl.gov/annotation/sequence/{ID}"
  
  $annotation$sequence$example
  [1] "http://api.metagenomics.anl.gov/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
  [2] "all annotated read sequences from mgm4447943.3 with hits in SwissProt organisms at evaule < e-10"         
  
  $annotation$sequence$name
  [1] "sequence"
  
  $annotation$sequence$description
  [1] "tab deliminted annotated sequence stream"
  
  $annotation$sequence$parameters
  $annotation$sequence$parameters$body
  named list()
  
  $annotation$sequence$parameters$options
  $annotation$sequence$parameters$options$source
  $annotation$sequence$parameters$options$source[[1]]
  [1] "cv"
  
  $annotation$sequence$parameters$options$source[[2]]
  $annotation$sequence$parameters$options$source[[2]][[1]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[2]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[3]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[4]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[5]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[6]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[7]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[8]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[9]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[10]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[11]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[12]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $annotation$sequence$parameters$options$source[[2]][[13]]
  [1] "Subsystems"                           
  [2] "ontology database, type ontology only"
  
  $annotation$sequence$parameters$options$source[[2]][[14]]
  [1] "NOG"                                  
  [2] "ontology database, type ontology only"
  
  $annotation$sequence$parameters$options$source[[2]][[15]]
  [1] "COG"                                  
  [2] "ontology database, type ontology only"
  
  $annotation$sequence$parameters$options$source[[2]][[16]]
  [1] "KO"                                   
  [2] "ontology database, type ontology only"
  
  
  
  $annotation$sequence$parameters$options$length
  [1] "int"                                                     
  [2] "value for minimum alignment length cutoff: default is 15"
  
  $annotation$sequence$parameters$options$identity
  [1] "int"                                                       
  [2] "percent value for minimum % identity cutoff: default is 60"
  
  $annotation$sequence$parameters$options$evalue
  [1] "int"                                                             
  [2] "negative exponent value for maximum e-value cutoff: default is 5"
  
  $annotation$sequence$parameters$options$filter
  [1] "string"                                                                   
  [2] "text string to filter annotations by: only return those that contain text"
  
  $annotation$sequence$parameters$options$type
  $annotation$sequence$parameters$options$type[[1]]
  [1] "cv"
  
  $annotation$sequence$parameters$options$type[[2]]
  $annotation$sequence$parameters$options$type[[2]][[1]]
  [1] "organism"             "return organism data"
  
  $annotation$sequence$parameters$options$type[[2]][[2]]
  [1] "function"             "return function data"
  
  $annotation$sequence$parameters$options$type[[2]][[3]]
  [1] "ontology"             "return ontology data"
  
  $annotation$sequence$parameters$options$type[[2]][[4]]
  [1] "feature"             "return feature data"
  
  $annotation$sequence$parameters$options$type[[2]][[5]]
  [1] "md5"                "return md5sum data"
  
  
  
  $annotation$sequence$parameters$options$filter_level
  [1] "string"                                                                  
  [2] "hierarchal level to filter annotations by, for organism or ontology only"
  
  
  $annotation$sequence$parameters$required
  $annotation$sequence$parameters$required$id
  [1] "string"                       "unique metagenome identifier"
  
  
  
  $annotation$sequence$method
  [1] "GET"
  
  $annotation$sequence$type
  [1] "stream"
  
  $annotation$sequence$attributes
  $annotation$sequence$attributes$`streaming text`
  $annotation$sequence$attributes$`streaming text`[[1]]
  [1] "object"
  
  $annotation$sequence$attributes$`streaming text`[[2]]
  $annotation$sequence$attributes$`streaming text`[[2]][[1]]
  $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_02
  [1] "string"           "m5nr id (md5sum)"
  
  $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_04
  [1] "string"                                 
  [2] "semicolon seperated list of annotations"
  
  $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_03
  [1] "string"       "dna sequence"
  
  $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_01
  [1] "string"      "sequence id"
  
  
  $annotation$sequence$attributes$`streaming text`[[2]][[2]]
  [1] "tab deliminted annotated sequence stream"
  
  
  
  
  
  $annotation$similarity
  $annotation$similarity$request
  [1] "http://api.metagenomics.anl.gov/annotation/similarity/{ID}"
  
  $annotation$similarity$example
  [1] "http://api.metagenomics.anl.gov/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO"
  [2] "all annotated read blat stats from mgm4447943.3 with hits in KO functions at % identity > 80"          
  
  $annotation$similarity$name
  [1] "similarity"
  
  $annotation$similarity$description
  [1] "tab deliminted blast m8 with annotation"
  
  $annotation$similarity$parameters
  $annotation$similarity$parameters$body
  named list()
  
  $annotation$similarity$parameters$options
  $annotation$similarity$parameters$options$source
  $annotation$similarity$parameters$options$source[[1]]
  [1] "cv"
  
  $annotation$similarity$parameters$options$source[[2]]
  $annotation$similarity$parameters$options$source[[2]][[1]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[2]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[3]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[4]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[5]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[6]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[7]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[8]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[9]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[10]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[11]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[12]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $annotation$similarity$parameters$options$source[[2]][[13]]
  [1] "Subsystems"                           
  [2] "ontology database, type ontology only"
  
  $annotation$similarity$parameters$options$source[[2]][[14]]
  [1] "NOG"                                  
  [2] "ontology database, type ontology only"
  
  $annotation$similarity$parameters$options$source[[2]][[15]]
  [1] "COG"                                  
  [2] "ontology database, type ontology only"
  
  $annotation$similarity$parameters$options$source[[2]][[16]]
  [1] "KO"                                   
  [2] "ontology database, type ontology only"
  
  
  
  $annotation$similarity$parameters$options$length
  [1] "int"                                                     
  [2] "value for minimum alignment length cutoff: default is 15"
  
  $annotation$similarity$parameters$options$identity
  [1] "int"                                                       
  [2] "percent value for minimum % identity cutoff: default is 60"
  
  $annotation$similarity$parameters$options$evalue
  [1] "int"                                                             
  [2] "negative exponent value for maximum e-value cutoff: default is 5"
  
  $annotation$similarity$parameters$options$filter
  [1] "string"                                                                   
  [2] "text string to filter annotations by: only return those that contain text"
  
  $annotation$similarity$parameters$options$type
  $annotation$similarity$parameters$options$type[[1]]
  [1] "cv"
  
  $annotation$similarity$parameters$options$type[[2]]
  $annotation$similarity$parameters$options$type[[2]][[1]]
  [1] "organism"             "return organism data"
  
  $annotation$similarity$parameters$options$type[[2]][[2]]
  [1] "function"             "return function data"
  
  $annotation$similarity$parameters$options$type[[2]][[3]]
  [1] "ontology"             "return ontology data"
  
  $annotation$similarity$parameters$options$type[[2]][[4]]
  [1] "feature"             "return feature data"
  
  $annotation$similarity$parameters$options$type[[2]][[5]]
  [1] "md5"                "return md5sum data"
  
  
  
  $annotation$similarity$parameters$options$filter_level
  [1] "string"                                                                  
  [2] "hierarchal level to filter annotations by, for organism or ontology only"
  
  
  $annotation$similarity$parameters$required
  $annotation$similarity$parameters$required$id
  [1] "string"                       "unique metagenome identifier"
  
  
  
  $annotation$similarity$method
  [1] "GET"
  
  $annotation$similarity$type
  [1] "stream"
  
  $annotation$similarity$attributes
  $annotation$similarity$attributes$`streaming text`
  $annotation$similarity$attributes$`streaming text`[[1]]
  [1] "object"
  
  $annotation$similarity$attributes$`streaming text`[[2]]
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_08
  [1] "int"       "query end"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_12
  [1] "float"     "bit score"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_02
  [1] "string"               "hit m5nr id (md5sum)"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_05
  [1] "int"                  "number of mismatches"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_07
  [1] "int"         "query start"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_11
  [1] "float"   "e-value"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_10
  [1] "int"     "hit end"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_04
  [1] "int"               "alignment length,"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_06
  [1] "int"                    "number of gap openings"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_09
  [1] "int"       "hit start"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_03
  [1] "float"               "percentage identity"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_13
  [1] "string"                                 
  [2] "semicolon seperated list of annotations"
  
  $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_01
  [1] "string"            "query sequence id"
  
  
  $annotation$similarity$attributes$`streaming text`[[2]][[2]]
  [1] "tab deliminted blast m8 with annotation"
  
  
  
  
  
  
  $compute
  $compute$info
  $compute$info$parameters
  $compute$info$parameters$body
  named list()
  
  $compute$info$parameters$required
  named list()
  
  $compute$info$parameters$options
  named list()
  
  
  $compute$info$request
  [1] "http://api.metagenomics.anl.gov/compute"
  
  $compute$info$name
  [1] "info"
  
  $compute$info$type
  [1] "synchronous"
  
  $compute$info$method
  [1] "GET"
  
  $compute$info$attributes
  [1] "self"
  
  $compute$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $compute$alphadiversity
  $compute$alphadiversity$request
  [1] "http://api.metagenomics.anl.gov/compute/alphadiversity/{ID}"
  
  $compute$alphadiversity$example
  [1] "http://api.metagenomics.anl.gov/compute/alphadiversity/mgm4447943.3?level=order"
  [2] "retrieve alpha diversity for order taxon"                                       
  
  $compute$alphadiversity$name
  [1] "alphadiversity"
  
  $compute$alphadiversity$description
  [1] "Calculate alpha diversity value for given ID and taxon level."
  
  $compute$alphadiversity$parameters
  $compute$alphadiversity$parameters$body
  named list()
  
  $compute$alphadiversity$parameters$required
  $compute$alphadiversity$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $compute$alphadiversity$parameters$options
  $compute$alphadiversity$parameters$options$source
  $compute$alphadiversity$parameters$options$source[[1]]
  [1] "cv"
  
  $compute$alphadiversity$parameters$options$source[[2]]
  $compute$alphadiversity$parameters$options$source[[2]][[1]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[2]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[3]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[4]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[5]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[6]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[7]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[8]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[9]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[10]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[11]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $compute$alphadiversity$parameters$options$source[[2]][[12]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  
  
  $compute$alphadiversity$parameters$options$level
  $compute$alphadiversity$parameters$options$level[[1]]
  [1] "cv"
  
  $compute$alphadiversity$parameters$options$level[[2]]
  $compute$alphadiversity$parameters$options$level[[2]][[1]]
  [1] "strain"                          "bottom organism taxanomic level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[2]]
  [1] "species"             "organism type level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[3]]
  [1] "genus"                    "organism taxanomic level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[4]]
  [1] "family"                   "organism taxanomic level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[5]]
  [1] "order"                    "organism taxanomic level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[6]]
  [1] "class"                    "organism taxanomic level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[7]]
  [1] "phylum"                   "organism taxanomic level"
  
  $compute$alphadiversity$parameters$options$level[[2]][[8]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  
  
  $compute$alphadiversity$method
  [1] "GET"
  
  $compute$alphadiversity$type
  [1] "synchronous"
  
  $compute$alphadiversity$attributes
  $compute$alphadiversity$attributes$url
  [1] "string"                                   
  [2] "resource location of this object instance"
  
  $compute$alphadiversity$attributes$data
  [1] "float"                 "alpha diversity value"
  
  $compute$alphadiversity$attributes$id
  [1] "string"                       "unique metagenome identifier"
  
  
  
  
  $download
  $download$info
  $download$info$parameters
  $download$info$parameters$body
  named list()
  
  $download$info$parameters$required
  named list()
  
  $download$info$parameters$options
  named list()
  
  
  $download$info$request
  [1] "http://api.metagenomics.anl.gov/download"
  
  $download$info$name
  [1] "info"
  
  $download$info$type
  [1] "synchronous"
  
  $download$info$method
  [1] "GET"
  
  $download$info$attributes
  [1] "self"
  
  $download$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $download$instance
  $download$instance$request
  [1] "http://api.metagenomics.anl.gov/download/{ID}"
  
  $download$instance$example
  [1] "http://api.metagenomics.anl.gov/download/mgm4447943.3?file=350.1"    
  [2] "download fasta file of genecalled protein sequences (from stage 350)"
  
  $download$instance$name
  [1] "instance"
  
  $download$instance$description
  [1] "Returns a single sequence file."
  
  $download$instance$parameters
  $download$instance$parameters$body
  named list()
  
  $download$instance$parameters$required
  $download$instance$parameters$required$id
  [1] "string"                       "unique metagenome identifier"
  
  
  $download$instance$parameters$options
  $download$instance$parameters$options$file
  [1] "string"                  "file name or identifier"
  
  
  
  $download$instance$method
  [1] "GET"
  
  $download$instance$type
  [1] "synchronous"
  
  $download$instance$attributes
  $download$instance$attributes$data
  [1] "file"                    "requested analysis file"
  
  
  
  $download$setlist
  $download$setlist$request
  [1] "http://api.metagenomics.anl.gov/download/{ID}"
  
  $download$setlist$example
  [1] "http://api.metagenomics.anl.gov/download/mgm4447943.3?stage=650"
  [2] "view all available files from stage 650"                        
  
  $download$setlist$name
  [1] "setlist"
  
  $download$setlist$description
  [1] "Returns a list of sets of sequence files for the given id."
  
  $download$setlist$parameters
  $download$setlist$parameters$body
  named list()
  
  $download$setlist$parameters$required
  $download$setlist$parameters$required$id
  [1] "string"                       "unique metagenome identifier"
  
  
  $download$setlist$parameters$options
  $download$setlist$parameters$options$stage
  [1] "string"                   "stage name or identifier"
  
  
  
  $download$setlist$method
  [1] "GET"
  
  $download$setlist$type
  [1] "synchronous"
  
  $download$setlist$attributes
  $download$setlist$attributes$stage_name
  [1] "string"                                      
  [2] "name of the stage in processing of this file"
  
  $download$setlist$attributes$file_name
  [1] "string"                    "name of the analysis file"
  
  $download$setlist$attributes$url
  [1] "string"                               
  [2] "url for retrieving this analysis file"
  
  $download$setlist$attributes$id
  [1] "string"                       "unique metagenome identifier"
  
  $download$setlist$attributes$file_id
  [1] "string"                             "unique identifier of file in stage"
  
  $download$setlist$attributes$stage_type
  [1] "string"                                                                                    
  [2] "type of the analysis file within a stage, i.e. passed or removed for quality control steps"
  
  $download$setlist$attributes$stage_id
  [1] "string"                                       
  [2] "three digit numerical identifier of the stage"
  
  
  
  
  $inbox
  $inbox$info
  $inbox$info$parameters
  $inbox$info$parameters$body
  named list()
  
  $inbox$info$parameters$required
  named list()
  
  $inbox$info$parameters$options
  named list()
  
  
  $inbox$info$request
  [1] "http://api.metagenomics.anl.gov/inbox"
  
  $inbox$info$name
  [1] "info"
  
  $inbox$info$type
  [1] "synchronous"
  
  $inbox$info$method
  [1] "GET"
  
  $inbox$info$attributes
  [1] "self"
  
  $inbox$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $inbox$view
  $inbox$view$request
  [1] "http://api.metagenomics.anl.gov/inbox"
  
  $inbox$view$example
  [1] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/inbox\""
  [2] "lists the contents of the user inbox, auth is required"                     
  
  $inbox$view$name
  [1] "view"
  
  $inbox$view$description
  [1] "lists the contents of the user inbox"
  
  $inbox$view$parameters
  $inbox$view$parameters$body
  named list()
  
  $inbox$view$parameters$required
  $inbox$view$parameters$required$auth
  [1] "string"                                                     
  [2] "unique string of text generated by MG-RAST for your account"
  
  
  $inbox$view$parameters$options
  named list()
  
  
  $inbox$view$method
  [1] "GET"
  
  $inbox$view$type
  [1] "synchronous"
  
  $inbox$view$attributes
  $inbox$view$attributes$timestamp
  [1] "string"                             "timestamp for return of this query"
  
  $inbox$view$attributes$files
  $inbox$view$attributes$files[[1]]
  [1] "list"
  
  $inbox$view$attributes$files[[2]]
  $inbox$view$attributes$files[[2]][[1]]
  [1] "object"
  
  $inbox$view$attributes$files[[2]][[2]]
  $inbox$view$attributes$files[[2]][[2]][[1]]
  $inbox$view$attributes$files[[2]][[2]][[1]]$filesize
  [1] "string"                     "disk size of file in bytes"
  
  $inbox$view$attributes$files[[2]][[2]][[1]]$timestamp
  [1] "string"            "timestamp of file"
  
  $inbox$view$attributes$files[[2]][[2]][[1]]$filename
  [1] "string"                              "path of file from within user inbox"
  
  
  $inbox$view$attributes$files[[2]][[2]][[2]]
  [1] "list of file objects"
  
  
  
  
  $inbox$view$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $inbox$view$attributes$id
  [1] "string"     "user login"
  
  
  
  
  $library
  $library$info
  $library$info$parameters
  $library$info$parameters$body
  named list()
  
  $library$info$parameters$required
  named list()
  
  $library$info$parameters$options
  named list()
  
  
  $library$info$request
  [1] "http://api.metagenomics.anl.gov/library"
  
  $library$info$name
  [1] "info"
  
  $library$info$type
  [1] "synchronous"
  
  $library$info$method
  [1] "GET"
  
  $library$info$attributes
  [1] "self"
  
  $library$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $library$query
  $library$query$request
  [1] "http://api.metagenomics.anl.gov/library"
  
  $library$query$example
  [1] "http://api.metagenomics.anl.gov/library?limit=20&order=name"
  [2] "retrieve the first 20 libraries ordered by name"            
  
  $library$query$name
  [1] "query"
  
  $library$query$description
  [1] "Returns a set of data matching the query criteria."
  
  $library$query$parameters
  $library$query$parameters$body
  named list()
  
  $library$query$parameters$required
  named list()
  
  $library$query$parameters$options
  $library$query$parameters$options$verbosity
  $library$query$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $library$query$parameters$options$verbosity[[2]]
  $library$query$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  
  
  $library$query$parameters$options$order
  $library$query$parameters$options$order[[1]]
  [1] "cv"
  
  $library$query$parameters$options$order[[2]]
  $library$query$parameters$options$order[[2]][[1]]
  [1] "id"                                "return data objects ordered by id"
  
  $library$query$parameters$options$order[[2]][[2]]
  [1] "name"                                "return data objects ordered by name"
  
  
  
  $library$query$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $library$query$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $library$query$method
  [1] "GET"
  
  $library$query$type
  [1] "synchronous"
  
  $library$query$attributes
  $library$query$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $library$query$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $library$query$attributes$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $library$query$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $library$query$attributes$data
  $library$query$attributes$data[[1]]
  [1] "list"
  
  $library$query$attributes$data[[2]]
  $library$query$attributes$data[[2]][[1]]
  [1] "object"
  
  $library$query$attributes$data[[2]][[2]]
  $library$query$attributes$data[[2]][[2]][[1]]
  $library$query$attributes$data[[2]][[2]][[1]]$version
  [1] "integer"               "version of the object"
  
  $library$query$attributes$data[[2]][[2]][[1]]$project
  [1] "reference project"               "reference to the project object"
  
  $library$query$attributes$data[[2]][[2]][[1]]$name
  [1] "string"                    "human readable identifier"
  
  $library$query$attributes$data[[2]][[2]][[1]]$sequencesets
  $library$query$attributes$data[[2]][[2]][[1]]$sequencesets[[1]]
  [1] "list"
  
  $library$query$attributes$data[[2]][[2]][[1]]$sequencesets[[2]]
  [1] "reference sequenceset"                            
  [2] "a list of references to the related sequence sets"
  
  
  $library$query$attributes$data[[2]][[2]][[1]]$metagenome
  [1] "reference metagenome"                      
  [2] "reference to the related metagenome object"
  
  $library$query$attributes$data[[2]][[2]][[1]]$created
  [1] "date"                              "time the object was first created"
  
  $library$query$attributes$data[[2]][[2]][[1]]$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $library$query$attributes$data[[2]][[2]][[1]]$id
  [1] "string"                   "unique object identifier"
  
  $library$query$attributes$data[[2]][[2]][[1]]$sample
  [1] "reference sample"                      
  [2] "reference to the related sample object"
  
  $library$query$attributes$data[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  
  $library$query$attributes$data[[2]][[2]][[2]]
  [1] "list of the library objects"
  
  
  
  
  $library$query$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  $library$query$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  
  
  $library$instance
  $library$instance$request
  [1] "http://api.metagenomics.anl.gov/library/{ID}"
  
  $library$instance$example
  [1] "http://api.metagenomics.anl.gov/library/mgl52924?verbosity=full"
  [2] "retrieve all data for library mgl52924"                         
  
  $library$instance$name
  [1] "instance"
  
  $library$instance$description
  [1] "Returns a single data object."
  
  $library$instance$parameters
  $library$instance$parameters$body
  named list()
  
  $library$instance$parameters$required
  $library$instance$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $library$instance$parameters$options
  $library$instance$parameters$options$verbosity
  $library$instance$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $library$instance$parameters$options$verbosity[[2]]
  $library$instance$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  $library$instance$parameters$options$verbosity[[2]][[2]]
  [1] "verbose"                                    
  [2] "returns a standard subselection of metadata"
  
  $library$instance$parameters$options$verbosity[[2]][[3]]
  [1] "full"                           "returns all connected metadata"
  
  
  
  
  
  $library$instance$method
  [1] "GET"
  
  $library$instance$type
  [1] "synchronous"
  
  $library$instance$attributes
  $library$instance$attributes$version
  [1] "integer"               "version of the object"
  
  $library$instance$attributes$project
  [1] "reference project"               "reference to the project object"
  
  $library$instance$attributes$name
  [1] "string"                    "human readable identifier"
  
  $library$instance$attributes$sequencesets
  $library$instance$attributes$sequencesets[[1]]
  [1] "list"
  
  $library$instance$attributes$sequencesets[[2]]
  [1] "reference sequenceset"                            
  [2] "a list of references to the related sequence sets"
  
  
  $library$instance$attributes$metagenome
  [1] "reference metagenome"                      
  [2] "reference to the related metagenome object"
  
  $library$instance$attributes$created
  [1] "date"                              "time the object was first created"
  
  $library$instance$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $library$instance$attributes$id
  [1] "string"                   "unique object identifier"
  
  $library$instance$attributes$sample
  [1] "reference sample"                      
  [2] "reference to the related sample object"
  
  $library$instance$attributes$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  
  
  
  $m5nr
  $m5nr$info
  $m5nr$info$parameters
  $m5nr$info$parameters$body
  named list()
  
  $m5nr$info$parameters$required
  named list()
  
  $m5nr$info$parameters$options
  named list()
  
  
  $m5nr$info$request
  [1] "http://api.metagenomics.anl.gov/m5nr"
  
  $m5nr$info$name
  [1] "info"
  
  $m5nr$info$type
  [1] "synchronous"
  
  $m5nr$info$method
  [1] "GET"
  
  $m5nr$info$attributes
  [1] "self"
  
  $m5nr$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $m5nr$ontology
  $m5nr$ontology$request
  [1] "http://api.metagenomics.anl.gov/m5nr/ontology"
  
  $m5nr$ontology$example
  [1] "http://api.metagenomics.anl.gov/m5nr/ontology?source=Subsystems&min_level=level3"
  [2] "retrieve subsystems hierarchy for the top 3 levels"                              
  
  $m5nr$ontology$name
  [1] "ontology"
  
  $m5nr$ontology$description
  [1] "Return functional hierarchy"
  
  $m5nr$ontology$parameters
  $m5nr$ontology$parameters$body
  named list()
  
  $m5nr$ontology$parameters$required
  named list()
  
  $m5nr$ontology$parameters$options
  $m5nr$ontology$parameters$options$source
  $m5nr$ontology$parameters$options$source[[1]]
  [1] "cv"
  
  $m5nr$ontology$parameters$options$source[[2]]
  $m5nr$ontology$parameters$options$source[[2]][[1]]
  [1] "Subsystems"                           
  [2] "ontology database, type ontology only"
  
  $m5nr$ontology$parameters$options$source[[2]][[2]]
  [1] "NOG"                                  
  [2] "ontology database, type ontology only"
  
  $m5nr$ontology$parameters$options$source[[2]][[3]]
  [1] "COG"                                  
  [2] "ontology database, type ontology only"
  
  $m5nr$ontology$parameters$options$source[[2]][[4]]
  [1] "KO"                                   
  [2] "ontology database, type ontology only"
  
  
  
  $m5nr$ontology$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$ontology$parameters$options$filter
  [1] "string"                                            
  [2] "text of ontology group (filter_level) to filter by"
  
  $m5nr$ontology$parameters$options$exact
  [1] "boolean"                                                                         
  [2] "if true return only those ontologies that exactly match filter, default is false"
  
  $m5nr$ontology$parameters$options$filter_level
  $m5nr$ontology$parameters$options$filter_level[[1]]
  [1] "cv"
  
  $m5nr$ontology$parameters$options$filter_level[[2]]
  $m5nr$ontology$parameters$options$filter_level[[2]][[1]]
  [1] "function"                       "bottom function ontology level"
  
  $m5nr$ontology$parameters$options$filter_level[[2]][[2]]
  [1] "level3"                  "function ontology level"
  
  $m5nr$ontology$parameters$options$filter_level[[2]][[3]]
  [1] "level2"                  "function ontology level"
  
  $m5nr$ontology$parameters$options$filter_level[[2]][[4]]
  [1] "level1"                      "top function ontology level"
  
  
  
  $m5nr$ontology$parameters$options$min_level
  $m5nr$ontology$parameters$options$min_level[[1]]
  [1] "cv"
  
  $m5nr$ontology$parameters$options$min_level[[2]]
  $m5nr$ontology$parameters$options$min_level[[2]][[1]]
  [1] "function"                       "bottom function ontology level"
  
  $m5nr$ontology$parameters$options$min_level[[2]][[2]]
  [1] "level3"                  "function ontology level"
  
  $m5nr$ontology$parameters$options$min_level[[2]][[3]]
  [1] "level2"                  "function ontology level"
  
  $m5nr$ontology$parameters$options$min_level[[2]][[4]]
  [1] "level1"                      "top function ontology level"
  
  
  
  
  
  $m5nr$ontology$method
  [1] "GET"
  
  $m5nr$ontology$type
  [1] "synchronous"
  
  $m5nr$ontology$attributes
  $m5nr$ontology$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$ontology$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$ontology$attributes$data
  $m5nr$ontology$attributes$data[[1]]
  [1] "list"
  
  $m5nr$ontology$attributes$data[[2]]
  $m5nr$ontology$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$ontology$attributes$data[[2]][[2]]
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level4
  [1] "string"                "ontology bottom level"
  
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level2
  [1] "string"           "ontology level 2"
  
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level3
  [1] "string"           "ontology level 3"
  
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]$id
  [1] "string"      "ontology ID"
  
  $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level1
  [1] "string"             "ontology top level"
  
  
  $m5nr$ontology$attributes$data[[2]][[2]][[2]]
  [1] "ontology object"
  
  
  
  
  
  
  $m5nr$taxonomy
  $m5nr$taxonomy$request
  [1] "http://api.metagenomics.anl.gov/m5nr/taxonomy"
  
  $m5nr$taxonomy$example
  [1] "http://api.metagenomics.anl.gov/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus"
  [2] "retrieve all class level taxa that belong to Bacteroidetes"                                            
  
  $m5nr$taxonomy$name
  [1] "taxonomy"
  
  $m5nr$taxonomy$description
  [1] "Return organism hierarchy"
  
  $m5nr$taxonomy$parameters
  $m5nr$taxonomy$parameters$body
  named list()
  
  $m5nr$taxonomy$parameters$required
  named list()
  
  $m5nr$taxonomy$parameters$options
  $m5nr$taxonomy$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$taxonomy$parameters$options$filter
  [1] "string"                                            
  [2] "text of taxanomy group (filter_level) to filter by"
  
  $m5nr$taxonomy$parameters$options$exact
  [1] "boolean"                                                                         
  [2] "if true return only those taxonomies that exactly match filter, default is false"
  
  $m5nr$taxonomy$parameters$options$filter_level
  $m5nr$taxonomy$parameters$options$filter_level[[1]]
  [1] "cv"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]]
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[1]]
  [1] "species"             "organism type level"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[2]]
  [1] "genus"                    "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[3]]
  [1] "family"                   "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[4]]
  [1] "order"                    "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[5]]
  [1] "class"                    "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[6]]
  [1] "phylum"                   "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$filter_level[[2]][[7]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  $m5nr$taxonomy$parameters$options$min_level
  $m5nr$taxonomy$parameters$options$min_level[[1]]
  [1] "cv"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]]
  $m5nr$taxonomy$parameters$options$min_level[[2]][[1]]
  [1] "species"             "organism type level"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]][[2]]
  [1] "genus"                    "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]][[3]]
  [1] "family"                   "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]][[4]]
  [1] "order"                    "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]][[5]]
  [1] "class"                    "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]][[6]]
  [1] "phylum"                   "organism taxanomic level"
  
  $m5nr$taxonomy$parameters$options$min_level[[2]][[7]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  
  
  $m5nr$taxonomy$method
  [1] "GET"
  
  $m5nr$taxonomy$type
  [1] "synchronous"
  
  $m5nr$taxonomy$attributes
  $m5nr$taxonomy$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$taxonomy$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$taxonomy$attributes$data
  $m5nr$taxonomy$attributes$data[[1]]
  [1] "list"
  
  $m5nr$taxonomy$attributes$data[[2]]
  $m5nr$taxonomy$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]]
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$genus
  [1] "string"         "organism genus"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"              "organism ncbi id"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$species
  [1] "string"           "organism species"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$domain
  [1] "string"          "organism domain"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$order
  [1] "string"         "organism order"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$class
  [1] "string"         "organism class"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$phylum
  [1] "string"          "organism phylum"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"        "organism name"
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$family
  [1] "string"          "organism family"
  
  
  $m5nr$taxonomy$attributes$data[[2]][[2]][[2]]
  [1] "taxonomy object"
  
  
  
  
  
  
  $m5nr$sources
  $m5nr$sources$request
  [1] "http://api.metagenomics.anl.gov/m5nr/sources"
  
  $m5nr$sources$example
  [1] "http://api.metagenomics.anl.gov/m5nr/sources"
  [2] "retrieve all data sources for M5NR"          
  
  $m5nr$sources$name
  [1] "sources"
  
  $m5nr$sources$description
  [1] "Return all sources in M5NR"
  
  $m5nr$sources$parameters
  $m5nr$sources$parameters$body
  named list()
  
  $m5nr$sources$parameters$required
  named list()
  
  $m5nr$sources$parameters$options
  $m5nr$sources$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  
  
  $m5nr$sources$method
  [1] "GET"
  
  $m5nr$sources$type
  [1] "synchronous"
  
  $m5nr$sources$attributes
  $m5nr$sources$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$sources$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$sources$attributes$data
  $m5nr$sources$attributes$data[[1]]
  [1] "list"
  
  $m5nr$sources$attributes$data[[2]]
  [1] "object"        "source object"
  
  
  
  
  $m5nr$accession
  $m5nr$accession$request
  [1] "http://api.metagenomics.anl.gov/m5nr/accession/{id}"
  
  $m5nr$accession$example
  [1] "http://api.metagenomics.anl.gov/m5nr/accession/YP_003268079.1"
  [2] "retrieve M5NR data for accession ID 'YP_003268079.1'"         
  
  $m5nr$accession$name
  [1] "accession"
  
  $m5nr$accession$description
  [1] "Return annotation of given source protein ID"
  
  $m5nr$accession$parameters
  $m5nr$accession$parameters$body
  named list()
  
  $m5nr$accession$parameters$required
  $m5nr$accession$parameters$required$id
  [1] "string"                           "unique identifier from source DB"
  
  
  $m5nr$accession$parameters$options
  $m5nr$accession$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$accession$parameters$options$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $m5nr$accession$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $m5nr$accession$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $m5nr$accession$method
  [1] "GET"
  
  $m5nr$accession$type
  [1] "synchronous"
  
  $m5nr$accession$attributes
  $m5nr$accession$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $m5nr$accession$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $m5nr$accession$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$accession$attributes$data
  $m5nr$accession$attributes$data[[1]]
  [1] "list"
  
  $m5nr$accession$attributes$data[[2]]
  $m5nr$accession$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$accession$attributes$data[[2]][[2]]
  $m5nr$accession$attributes$data[[2]][[2]][[1]]
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$`function`
  [1] "string"              "function annotation"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$type
  [1] "string"      "source type"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"                  "organism ncbi tax_id"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"              "organism annotation"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$md5
  [1] "string"                 "md5 checksum - M5NR ID"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$alias
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$alias[[1]]
  [1] "list"
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$alias[[2]]
  [1] "string"          "db_xref alaises"
  
  
  $m5nr$accession$attributes$data[[2]][[2]][[1]]$accession
  [1] "string"                            "unique identifier given by source"
  
  
  $m5nr$accession$attributes$data[[2]][[2]][[2]]
  [1] "annotation object"
  
  
  
  
  $m5nr$accession$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $m5nr$accession$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$accession$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $m5nr$accession$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  $m5nr$alias
  $m5nr$alias$request
  [1] "http://api.metagenomics.anl.gov/m5nr/alias/{text}"
  
  $m5nr$alias$example
  [1] "http://api.metagenomics.anl.gov/m5nr/alias/IPR001478"
  [2] "retrieve M5NR data for db_xref ID 'IPR001478'"       
  
  $m5nr$alias$name
  [1] "alias"
  
  $m5nr$alias$description
  [1] "Return annotations for alias IDs containing the given text"
  
  $m5nr$alias$parameters
  $m5nr$alias$parameters$body
  named list()
  
  $m5nr$alias$parameters$required
  $m5nr$alias$parameters$required$text
  [1] "string"                       "text string of partial alias"
  
  
  $m5nr$alias$parameters$options
  $m5nr$alias$parameters$options$source
  [1] "string"                            "source name to restrict search by"
  
  $m5nr$alias$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$alias$parameters$options$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $m5nr$alias$parameters$options$exact
  [1] "boolean"                                                                              
  [2] "if true return only those annotations that exactly match input text, default is false"
  
  $m5nr$alias$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $m5nr$alias$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $m5nr$alias$method
  [1] "GET"
  
  $m5nr$alias$type
  [1] "synchronous"
  
  $m5nr$alias$attributes
  $m5nr$alias$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $m5nr$alias$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $m5nr$alias$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$alias$attributes$data
  $m5nr$alias$attributes$data[[1]]
  [1] "list"
  
  $m5nr$alias$attributes$data[[2]]
  $m5nr$alias$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$alias$attributes$data[[2]][[2]]
  $m5nr$alias$attributes$data[[2]][[2]][[1]]
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$`function`
  [1] "string"              "function annotation"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$type
  [1] "string"      "source type"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"                  "organism ncbi tax_id"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"              "organism annotation"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$md5
  [1] "string"                 "md5 checksum - M5NR ID"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$alias
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$alias[[1]]
  [1] "list"
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$alias[[2]]
  [1] "string"          "db_xref alaises"
  
  
  $m5nr$alias$attributes$data[[2]][[2]][[1]]$accession
  [1] "string"                            "unique identifier given by source"
  
  
  $m5nr$alias$attributes$data[[2]][[2]][[2]]
  [1] "annotation object"
  
  
  
  
  $m5nr$alias$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $m5nr$alias$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$alias$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $m5nr$alias$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  $m5nr$md5
  $m5nr$md5$request
  [1] "http://api.metagenomics.anl.gov/m5nr/md5/{id}"
  
  $m5nr$md5$example
  [1] "http://api.metagenomics.anl.gov/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro"
  [2] "retrieve InterPro M5NR data for md5sum '000821a2e2f63df1a3873e4b280002a8'"                
  
  $m5nr$md5$name
  [1] "md5"
  
  $m5nr$md5$description
  [1] "Return annotation(s) or sequence of given md5sum (M5NR ID)"
  
  $m5nr$md5$parameters
  $m5nr$md5$parameters$body
  named list()
  
  $m5nr$md5$parameters$required
  $m5nr$md5$parameters$required$id
  [1] "string"                                   
  [2] "unique identifier in form of md5 checksum"
  
  
  $m5nr$md5$parameters$options
  $m5nr$md5$parameters$options$source
  [1] "string"                            "source name to restrict search by"
  
  $m5nr$md5$parameters$options$format
  $m5nr$md5$parameters$options$format[[1]]
  [1] "cv"
  
  $m5nr$md5$parameters$options$format[[2]]
  $m5nr$md5$parameters$options$format[[2]][[1]]
  [1] "fasta"                            "return sequences in fasta format"
  
  $m5nr$md5$parameters$options$format[[2]][[2]]
  [1] "json"                            "return sequences in json struct"
  
  
  
  $m5nr$md5$parameters$options$sequence
  [1] "boolean"                                                                        
  [2] "if true return sequence output, else return annotation output, default is false"
  
  $m5nr$md5$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$md5$parameters$options$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $m5nr$md5$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $m5nr$md5$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $m5nr$md5$method
  [1] "GET"
  
  $m5nr$md5$type
  [1] "synchronous"
  
  $m5nr$md5$attributes
  $m5nr$md5$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $m5nr$md5$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $m5nr$md5$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$md5$attributes$data
  $m5nr$md5$attributes$data[[1]]
  [1] "list"
  
  $m5nr$md5$attributes$data[[2]]
  $m5nr$md5$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$md5$attributes$data[[2]][[2]]
  $m5nr$md5$attributes$data[[2]][[2]][[1]]
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$`function`
  [1] "string"              "function annotation"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$type
  [1] "string"      "source type"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"                  "organism ncbi tax_id"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"              "organism annotation"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$md5
  [1] "string"                 "md5 checksum - M5NR ID"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$alias
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$alias[[1]]
  [1] "list"
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$alias[[2]]
  [1] "string"          "db_xref alaises"
  
  
  $m5nr$md5$attributes$data[[2]][[2]][[1]]$accession
  [1] "string"                            "unique identifier given by source"
  
  
  $m5nr$md5$attributes$data[[2]][[2]][[2]]
  [1] "annotation object"
  
  
  
  
  $m5nr$md5$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $m5nr$md5$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$md5$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $m5nr$md5$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  $m5nr$`function`
  $m5nr$`function`$request
  [1] "http://api.metagenomics.anl.gov/m5nr/function/{text}"
  
  $m5nr$`function`$example
  [1] "http://api.metagenomics.anl.gov/m5nr/function/sulfatase?source=GenBank"     
  [2] "retrieve GenBank M5NR data for function names containing string 'sulfatase'"
  
  $m5nr$`function`$name
  [1] "function"
  
  $m5nr$`function`$description
  [1] "Return annotations for function names containing the given text"
  
  $m5nr$`function`$parameters
  $m5nr$`function`$parameters$body
  named list()
  
  $m5nr$`function`$parameters$required
  $m5nr$`function`$parameters$required$text
  [1] "string"                              
  [2] "text string of partial function name"
  
  
  $m5nr$`function`$parameters$options
  $m5nr$`function`$parameters$options$source
  [1] "string"                            "source name to restrict search by"
  
  $m5nr$`function`$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$`function`$parameters$options$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $m5nr$`function`$parameters$options$exact
  [1] "boolean"                                                                              
  [2] "if true return only those annotations that exactly match input text, default is false"
  
  $m5nr$`function`$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $m5nr$`function`$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  $m5nr$`function`$parameters$options$inverse
  [1] "boolean"                                                                             
  [2] "if true return only those annotations that do not match input text, default is false"
  
  
  
  $m5nr$`function`$method
  [1] "GET"
  
  $m5nr$`function`$type
  [1] "synchronous"
  
  $m5nr$`function`$attributes
  $m5nr$`function`$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $m5nr$`function`$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $m5nr$`function`$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$`function`$attributes$data
  $m5nr$`function`$attributes$data[[1]]
  [1] "list"
  
  $m5nr$`function`$attributes$data[[2]]
  $m5nr$`function`$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$`function`$attributes$data[[2]][[2]]
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$`function`
  [1] "string"              "function annotation"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$type
  [1] "string"      "source type"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"                  "organism ncbi tax_id"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"              "organism annotation"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$md5
  [1] "string"                 "md5 checksum - M5NR ID"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$alias
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$alias[[1]]
  [1] "list"
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$alias[[2]]
  [1] "string"          "db_xref alaises"
  
  
  $m5nr$`function`$attributes$data[[2]][[2]][[1]]$accession
  [1] "string"                            "unique identifier given by source"
  
  
  $m5nr$`function`$attributes$data[[2]][[2]][[2]]
  [1] "annotation object"
  
  
  
  
  $m5nr$`function`$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $m5nr$`function`$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$`function`$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $m5nr$`function`$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  $m5nr$organism
  $m5nr$organism$request
  [1] "http://api.metagenomics.anl.gov/m5nr/organism/{text}"
  
  $m5nr$organism$example
  [1] "http://api.metagenomics.anl.gov/m5nr/organism/akkermansia?source=KEGG"     
  [2] "retrieve KEGG M5NR data for organism names containing string 'akkermansia'"
  
  $m5nr$organism$name
  [1] "organism"
  
  $m5nr$organism$description
  [1] "Return annotations for organism names containing the given text"
  
  $m5nr$organism$parameters
  $m5nr$organism$parameters$body
  named list()
  
  $m5nr$organism$parameters$required
  $m5nr$organism$parameters$required$text
  [1] "string"                              
  [2] "text string of partial organism name"
  
  
  $m5nr$organism$parameters$options
  $m5nr$organism$parameters$options$source
  [1] "string"                            "source name to restrict search by"
  
  $m5nr$organism$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$organism$parameters$options$exact
  [1] "boolean"                                                                              
  [2] "if true return only those annotations that exactly match input text, default is false"
  
  $m5nr$organism$parameters$options$inverse
  [1] "boolean"                                                                             
  [2] "if true return only those annotations that do not match input text, default is false"
  
  $m5nr$organism$parameters$options$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $m5nr$organism$parameters$options$tax_level
  $m5nr$organism$parameters$options$tax_level[[1]]
  [1] "cv"
  
  $m5nr$organism$parameters$options$tax_level[[2]]
  $m5nr$organism$parameters$options$tax_level[[2]][[1]]
  [1] "strain"                          "bottom organism taxanomic level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[2]]
  [1] "species"             "organism type level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[3]]
  [1] "genus"                    "organism taxanomic level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[4]]
  [1] "family"                   "organism taxanomic level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[5]]
  [1] "order"                    "organism taxanomic level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[6]]
  [1] "class"                    "organism taxanomic level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[7]]
  [1] "phylum"                   "organism taxanomic level"
  
  $m5nr$organism$parameters$options$tax_level[[2]][[8]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  $m5nr$organism$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $m5nr$organism$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $m5nr$organism$method
  [1] "GET"
  
  $m5nr$organism$type
  [1] "synchronous"
  
  $m5nr$organism$attributes
  $m5nr$organism$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $m5nr$organism$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $m5nr$organism$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$organism$attributes$data
  $m5nr$organism$attributes$data[[1]]
  [1] "list"
  
  $m5nr$organism$attributes$data[[2]]
  $m5nr$organism$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$organism$attributes$data[[2]][[2]]
  $m5nr$organism$attributes$data[[2]][[2]][[1]]
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$`function`
  [1] "string"              "function annotation"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$type
  [1] "string"      "source type"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"                  "organism ncbi tax_id"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"              "organism annotation"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$md5
  [1] "string"                 "md5 checksum - M5NR ID"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$alias
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$alias[[1]]
  [1] "list"
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$alias[[2]]
  [1] "string"          "db_xref alaises"
  
  
  $m5nr$organism$attributes$data[[2]][[2]][[1]]$accession
  [1] "string"                            "unique identifier given by source"
  
  
  $m5nr$organism$attributes$data[[2]][[2]][[2]]
  [1] "annotation object"
  
  
  
  
  $m5nr$organism$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $m5nr$organism$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$organism$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $m5nr$organism$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  $m5nr$sequence
  $m5nr$sequence$request
  [1] "http://api.metagenomics.anl.gov/m5nr/sequence/{text}"
  
  $m5nr$sequence$example
  [1] "http://api.metagenomics.anl.gov/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL"
  [2] "retrieve TrEMBL M5NR data for md5sum of sequence 'MAGENHQWQGSIL'"         
  
  $m5nr$sequence$name
  [1] "sequence"
  
  $m5nr$sequence$description
  [1] "Return annotation(s) for md5sum (M5NR ID) of given sequence"
  
  $m5nr$sequence$parameters
  $m5nr$sequence$parameters$body
  named list()
  
  $m5nr$sequence$parameters$required
  $m5nr$sequence$parameters$required$text
  [1] "string"                          "text string of protein sequence"
  
  
  $m5nr$sequence$parameters$options
  $m5nr$sequence$parameters$options$source
  [1] "string"                            "source name to restrict search by"
  
  $m5nr$sequence$parameters$options$version
  [1] "integer"                  "M5NR version, default 10"
  
  $m5nr$sequence$parameters$options$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $m5nr$sequence$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $m5nr$sequence$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $m5nr$sequence$method
  [1] "GET"
  
  $m5nr$sequence$type
  [1] "synchronous"
  
  $m5nr$sequence$attributes
  $m5nr$sequence$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $m5nr$sequence$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $m5nr$sequence$attributes$version
  [1] "integer"         "version of M5NR"
  
  $m5nr$sequence$attributes$data
  $m5nr$sequence$attributes$data[[1]]
  [1] "list"
  
  $m5nr$sequence$attributes$data[[2]]
  $m5nr$sequence$attributes$data[[2]][[1]]
  [1] "object"
  
  $m5nr$sequence$attributes$data[[2]][[2]]
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$source
  [1] "string"      "source name"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$`function`
  [1] "string"              "function annotation"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$type
  [1] "string"      "source type"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
  [1] "int"                  "organism ncbi tax_id"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$organism
  [1] "string"              "organism annotation"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$md5
  [1] "string"                 "md5 checksum - M5NR ID"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$alias
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$alias[[1]]
  [1] "list"
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$alias[[2]]
  [1] "string"          "db_xref alaises"
  
  
  $m5nr$sequence$attributes$data[[2]][[2]][[1]]$accession
  [1] "string"                            "unique identifier given by source"
  
  
  $m5nr$sequence$attributes$data[[2]][[2]][[2]]
  [1] "annotation object"
  
  
  
  
  $m5nr$sequence$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $m5nr$sequence$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $m5nr$sequence$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $m5nr$sequence$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  
  $matrix
  $matrix$info
  $matrix$info$parameters
  $matrix$info$parameters$body
  named list()
  
  $matrix$info$parameters$required
  named list()
  
  $matrix$info$parameters$options
  named list()
  
  
  $matrix$info$request
  [1] "http://api.metagenomics.anl.gov/matrix"
  
  $matrix$info$name
  [1] "info"
  
  $matrix$info$type
  [1] "synchronous"
  
  $matrix$info$method
  [1] "GET"
  
  $matrix$info$attributes
  [1] "self"
  
  $matrix$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $matrix$organism
  $matrix$organism$request
  [1] "http://api.metagenomics.anl.gov/matrix/organism"
  
  $matrix$organism$example
  [1] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=family&source=RefSeq&result_type=abundance&evalue=15"
  [2] "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"                                                                 
  
  $matrix$organism$name
  [1] "organism"
  
  $matrix$organism$description
  [1] "Returns a BIOM object."
  
  $matrix$organism$parameters
  $matrix$organism$parameters$body
  named list()
  
  $matrix$organism$parameters$required
  named list()
  
  $matrix$organism$parameters$options
  $matrix$organism$parameters$options$asynchronous
  [1] "boolean"                                                                         
  [2] "if true return process id to query status resource for results, default is false"
  
  $matrix$organism$parameters$options$source
  $matrix$organism$parameters$options$source[[1]]
  [1] "cv"
  
  $matrix$organism$parameters$options$source[[2]]
  $matrix$organism$parameters$options$source[[2]][[1]]
  [1] "M5NR"                           "comprehensive protein database"
  
  $matrix$organism$parameters$options$source[[2]][[2]]
  [1] "M5RNA"                      "comprehensive RNA database"
  
  $matrix$organism$parameters$options$source[[2]][[3]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[4]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[5]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[6]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[7]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[8]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[9]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[10]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[11]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[12]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[13]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $matrix$organism$parameters$options$source[[2]][[14]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  
  
  $matrix$organism$parameters$options$result_type
  $matrix$organism$parameters$options$result_type[[1]]
  [1] "cv"
  
  $matrix$organism$parameters$options$result_type[[2]]
  $matrix$organism$parameters$options$result_type[[2]][[1]]
  [1] "abundance"                              
  [2] "number of reads with hits in annotation"
  
  $matrix$organism$parameters$options$result_type[[2]][[2]]
  [1] "evalue"                                        
  [2] "average e-value exponent of hits in annotation"
  
  $matrix$organism$parameters$options$result_type[[2]][[3]]
  [1] "identity"                                      
  [2] "average percent identity of hits in annotation"
  
  $matrix$organism$parameters$options$result_type[[2]][[4]]
  [1] "length"                                        
  [2] "average alignment length of hits in annotation"
  
  
  
  $matrix$organism$parameters$options$filter
  [1] "string"                                                                                
  [2] "filter the return results to only include abundances based on genes with this function"
  
  $matrix$organism$parameters$options$group_level
  $matrix$organism$parameters$options$group_level[[1]]
  [1] "cv"
  
  $matrix$organism$parameters$options$group_level[[2]]
  $matrix$organism$parameters$options$group_level[[2]][[1]]
  [1] "strain"                          "bottom organism taxanomic level"
  
  $matrix$organism$parameters$options$group_level[[2]][[2]]
  [1] "species"             "organism type level"
  
  $matrix$organism$parameters$options$group_level[[2]][[3]]
  [1] "genus"                    "organism taxanomic level"
  
  $matrix$organism$parameters$options$group_level[[2]][[4]]
  [1] "family"                   "organism taxanomic level"
  
  $matrix$organism$parameters$options$group_level[[2]][[5]]
  [1] "order"                    "organism taxanomic level"
  
  $matrix$organism$parameters$options$group_level[[2]][[6]]
  [1] "class"                    "organism taxanomic level"
  
  $matrix$organism$parameters$options$group_level[[2]][[7]]
  [1] "phylum"                   "organism taxanomic level"
  
  $matrix$organism$parameters$options$group_level[[2]][[8]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  $matrix$organism$parameters$options$taxid
  [1] "boolean"                                                                          
  [2] "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
  
  $matrix$organism$parameters$options$grep
  [1] "string"                                                                      
  [2] "filter the return results to only include annotations that contain this text"
  
  $matrix$organism$parameters$options$length
  [1] "int"                                                     
  [2] "value for minimum alignment length cutoff: default is 15"
  
  $matrix$organism$parameters$options$evalue
  [1] "int"                                                             
  [2] "negative exponent value for maximum e-value cutoff: default is 5"
  
  $matrix$organism$parameters$options$identity
  [1] "int"                                                       
  [2] "percent value for minimum % identity cutoff: default is 60"
  
  $matrix$organism$parameters$options$filter_source
  $matrix$organism$parameters$options$filter_source[[1]]
  [1] "cv"
  
  $matrix$organism$parameters$options$filter_source[[2]]
  $matrix$organism$parameters$options$filter_source[[2]][[1]]
  [1] "Subsystems"                           
  [2] "ontology database, type ontology only"
  
  $matrix$organism$parameters$options$filter_source[[2]][[2]]
  [1] "NOG"                                  
  [2] "ontology database, type ontology only"
  
  $matrix$organism$parameters$options$filter_source[[2]][[3]]
  [1] "COG"                                  
  [2] "ontology database, type ontology only"
  
  $matrix$organism$parameters$options$filter_source[[2]][[4]]
  [1] "KO"                                   
  [2] "ontology database, type ontology only"
  
  
  
  $matrix$organism$parameters$options$hide_metadata
  [1] "boolean"                                                                        
  [2] "if true do not return metagenome metadata in 'columns' object, default is false"
  
  $matrix$organism$parameters$options$id
  [1] "string"                                             
  [2] "one or more metagenome or project unique identifier"
  
  $matrix$organism$parameters$options$filter_level
  $matrix$organism$parameters$options$filter_level[[1]]
  [1] "cv"
  
  $matrix$organism$parameters$options$filter_level[[2]]
  $matrix$organism$parameters$options$filter_level[[2]][[1]]
  [1] "function"                       "bottom function ontology level"
  
  $matrix$organism$parameters$options$filter_level[[2]][[2]]
  [1] "level3"                  "function ontology level"
  
  $matrix$organism$parameters$options$filter_level[[2]][[3]]
  [1] "level2"                  "function ontology level"
  
  $matrix$organism$parameters$options$filter_level[[2]][[4]]
  [1] "level1"                      "top function ontology level"
  
  
  
  $matrix$organism$parameters$options$hit_type
  $matrix$organism$parameters$options$hit_type[[1]]
  [1] "cv"
  
  $matrix$organism$parameters$options$hit_type[[2]]
  $matrix$organism$parameters$options$hit_type[[2]][[1]]
  [1] "all"                                                                        
  [2] "returns results based on all organisms that map to top hit per read-feature"
  
  $matrix$organism$parameters$options$hit_type[[2]][[2]]
  [1] "single"                                                                 
  [2] "returns results based on a single organism for top hit per read-feature"
  
  $matrix$organism$parameters$options$hit_type[[2]][[3]]
  [1] "lca"                                                                                                                        
  [2] "returns results based on the Least Common Ancestor for all organisms (M5NR+M5RNA only) that map to hits from a read-feature"
  
  
  
  
  
  $matrix$organism$method
  [1] "GET"
  
  $matrix$organism$type
  [1] "synchronous or asynchronous"
  
  $matrix$organism$attributes
  $matrix$organism$attributes$generated_by
  [1] "string"                           "identifier of the data generator"
  
  $matrix$organism$attributes$matrix_type
  [1] "string"                                            
  [2] "type of the data encoding matrix (dense or sparse)"
  
  $matrix$organism$attributes$date
  [1] "date"                               "time the output data was generated"
  
  $matrix$organism$attributes$data
  $matrix$organism$attributes$data[[1]]
  [1] "list"
  
  $matrix$organism$attributes$data[[2]]
  $matrix$organism$attributes$data[[2]][[1]]
  [1] "list"
  
  $matrix$organism$attributes$data[[2]][[2]]
  [1] "float"             "the matrix values"
  
  
  
  $matrix$organism$attributes$rows
  $matrix$organism$attributes$rows[[1]]
  [1] "list"
  
  $matrix$organism$attributes$rows[[2]]
  $matrix$organism$attributes$rows[[2]][[1]]
  [1] "object"
  
  $matrix$organism$attributes$rows[[2]][[2]]
  $matrix$organism$attributes$rows[[2]][[2]][[1]]
  $matrix$organism$attributes$rows[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $matrix$organism$attributes$rows[[2]][[2]][[1]]$id
  [1] "string"                 "unique annotation text"
  
  
  $matrix$organism$attributes$rows[[2]][[2]][[2]]
  [1] "rows object"
  
  
  
  
  $matrix$organism$attributes$matrix_element_value
  [1] "string"                                          
  [2] "result_type of the elements in the return matrix"
  
  $matrix$organism$attributes$matrix_element_type
  [1] "string"                                        
  [2] "data type of the elements in the return matrix"
  
  $matrix$organism$attributes$format_url
  [1] "string"                          "url to the format specification"
  
  $matrix$organism$attributes$format
  [1] "string"                    "format specification name"
  
  $matrix$organism$attributes$columns
  $matrix$organism$attributes$columns[[1]]
  [1] "list"
  
  $matrix$organism$attributes$columns[[2]]
  $matrix$organism$attributes$columns[[2]][[1]]
  [1] "object"
  
  $matrix$organism$attributes$columns[[2]][[2]]
  $matrix$organism$attributes$columns[[2]][[2]][[1]]
  $matrix$organism$attributes$columns[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $matrix$organism$attributes$columns[[2]][[2]][[1]]$id
  [1] "string"                       "unique metagenome identifier"
  
  
  $matrix$organism$attributes$columns[[2]][[2]][[2]]
  [1] "columns object"
  
  
  
  
  $matrix$organism$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $matrix$organism$attributes$shape
  $matrix$organism$attributes$shape[[1]]
  [1] "list"
  
  $matrix$organism$attributes$shape[[2]]
  [1] "integer"                                         
  [2] "list of the dimension sizes of the return matrix"
  
  
  $matrix$organism$attributes$id
  [1] "string"                   "unique object identifier"
  
  $matrix$organism$attributes$type
  [1] "string"                                                        
  [2] "type of the data in the return table (taxon, function or gene)"
  
  
  
  $matrix$`function`
  $matrix$`function`$request
  [1] "http://api.metagenomics.anl.gov/matrix/function"
  
  $matrix$`function`$example
  [1] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=level3&source=Subsystems&result_type=abundance&identity=80&filter_level=phylum&filter=Firmicutes"
  [2] "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtered to return annotations only in phylum Firmicutes"                                                            
  
  $matrix$`function`$name
  [1] "function"
  
  $matrix$`function`$description
  [1] "Returns a BIOM object."
  
  $matrix$`function`$parameters
  $matrix$`function`$parameters$body
  named list()
  
  $matrix$`function`$parameters$required
  named list()
  
  $matrix$`function`$parameters$options
  $matrix$`function`$parameters$options$asynchronous
  [1] "boolean"                                                                         
  [2] "if true return process id to query status resource for results, default is false"
  
  $matrix$`function`$parameters$options$source
  $matrix$`function`$parameters$options$source[[1]]
  [1] "cv"
  
  $matrix$`function`$parameters$options$source[[2]]
  $matrix$`function`$parameters$options$source[[2]][[1]]
  [1] "Subsystems"                           
  [2] "ontology database, type ontology only"
  
  $matrix$`function`$parameters$options$source[[2]][[2]]
  [1] "NOG"                                  
  [2] "ontology database, type ontology only"
  
  $matrix$`function`$parameters$options$source[[2]][[3]]
  [1] "COG"                                  
  [2] "ontology database, type ontology only"
  
  $matrix$`function`$parameters$options$source[[2]][[4]]
  [1] "KO"                                   
  [2] "ontology database, type ontology only"
  
  
  
  $matrix$`function`$parameters$options$result_type
  $matrix$`function`$parameters$options$result_type[[1]]
  [1] "cv"
  
  $matrix$`function`$parameters$options$result_type[[2]]
  $matrix$`function`$parameters$options$result_type[[2]][[1]]
  [1] "abundance"                              
  [2] "number of reads with hits in annotation"
  
  $matrix$`function`$parameters$options$result_type[[2]][[2]]
  [1] "evalue"                                        
  [2] "average e-value exponent of hits in annotation"
  
  $matrix$`function`$parameters$options$result_type[[2]][[3]]
  [1] "identity"                                      
  [2] "average percent identity of hits in annotation"
  
  $matrix$`function`$parameters$options$result_type[[2]][[4]]
  [1] "length"                                        
  [2] "average alignment length of hits in annotation"
  
  
  
  $matrix$`function`$parameters$options$filter
  [1] "string"                                                                                
  [2] "filter the return results to only include abundances based on genes with this organism"
  
  $matrix$`function`$parameters$options$group_level
  $matrix$`function`$parameters$options$group_level[[1]]
  [1] "cv"
  
  $matrix$`function`$parameters$options$group_level[[2]]
  $matrix$`function`$parameters$options$group_level[[2]][[1]]
  [1] "function"                       "bottom function ontology level"
  
  $matrix$`function`$parameters$options$group_level[[2]][[2]]
  [1] "level3"                  "function ontology level"
  
  $matrix$`function`$parameters$options$group_level[[2]][[3]]
  [1] "level2"                  "function ontology level"
  
  $matrix$`function`$parameters$options$group_level[[2]][[4]]
  [1] "level1"                      "top function ontology level"
  
  
  
  $matrix$`function`$parameters$options$grep
  [1] "string"                                                                      
  [2] "filter the return results to only include annotations that contain this text"
  
  $matrix$`function`$parameters$options$length
  [1] "int"                                                     
  [2] "value for minimum alignment length cutoff: default is 15"
  
  $matrix$`function`$parameters$options$evalue
  [1] "int"                                                             
  [2] "negative exponent value for maximum e-value cutoff: default is 5"
  
  $matrix$`function`$parameters$options$identity
  [1] "int"                                                       
  [2] "percent value for minimum % identity cutoff: default is 60"
  
  $matrix$`function`$parameters$options$filter_source
  $matrix$`function`$parameters$options$filter_source[[1]]
  [1] "cv"
  
  $matrix$`function`$parameters$options$filter_source[[2]]
  $matrix$`function`$parameters$options$filter_source[[2]][[1]]
  [1] "M5NR"                           "comprehensive protein database"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[2]]
  [1] "M5RNA"                      "comprehensive RNA database"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[3]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[4]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[5]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[6]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[7]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[8]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[9]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[10]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[11]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[12]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[13]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $matrix$`function`$parameters$options$filter_source[[2]][[14]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  
  
  $matrix$`function`$parameters$options$hide_metadata
  [1] "boolean"                                                                        
  [2] "if true do not return metagenome metadata in 'columns' object, default is false"
  
  $matrix$`function`$parameters$options$id
  [1] "string"                                             
  [2] "one or more metagenome or project unique identifier"
  
  $matrix$`function`$parameters$options$filter_level
  $matrix$`function`$parameters$options$filter_level[[1]]
  [1] "cv"
  
  $matrix$`function`$parameters$options$filter_level[[2]]
  $matrix$`function`$parameters$options$filter_level[[2]][[1]]
  [1] "strain"                          "bottom organism taxanomic level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[2]]
  [1] "species"             "organism type level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[3]]
  [1] "genus"                    "organism taxanomic level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[4]]
  [1] "family"                   "organism taxanomic level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[5]]
  [1] "order"                    "organism taxanomic level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[6]]
  [1] "class"                    "organism taxanomic level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[7]]
  [1] "phylum"                   "organism taxanomic level"
  
  $matrix$`function`$parameters$options$filter_level[[2]][[8]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  
  
  $matrix$`function`$method
  [1] "GET"
  
  $matrix$`function`$type
  [1] "synchronous or asynchronous"
  
  $matrix$`function`$attributes
  $matrix$`function`$attributes$generated_by
  [1] "string"                           "identifier of the data generator"
  
  $matrix$`function`$attributes$matrix_type
  [1] "string"                                            
  [2] "type of the data encoding matrix (dense or sparse)"
  
  $matrix$`function`$attributes$date
  [1] "date"                               "time the output data was generated"
  
  $matrix$`function`$attributes$data
  $matrix$`function`$attributes$data[[1]]
  [1] "list"
  
  $matrix$`function`$attributes$data[[2]]
  $matrix$`function`$attributes$data[[2]][[1]]
  [1] "list"
  
  $matrix$`function`$attributes$data[[2]][[2]]
  [1] "float"             "the matrix values"
  
  
  
  $matrix$`function`$attributes$rows
  $matrix$`function`$attributes$rows[[1]]
  [1] "list"
  
  $matrix$`function`$attributes$rows[[2]]
  $matrix$`function`$attributes$rows[[2]][[1]]
  [1] "object"
  
  $matrix$`function`$attributes$rows[[2]][[2]]
  $matrix$`function`$attributes$rows[[2]][[2]][[1]]
  $matrix$`function`$attributes$rows[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $matrix$`function`$attributes$rows[[2]][[2]][[1]]$id
  [1] "string"                 "unique annotation text"
  
  
  $matrix$`function`$attributes$rows[[2]][[2]][[2]]
  [1] "rows object"
  
  
  
  
  $matrix$`function`$attributes$matrix_element_value
  [1] "string"                                          
  [2] "result_type of the elements in the return matrix"
  
  $matrix$`function`$attributes$matrix_element_type
  [1] "string"                                        
  [2] "data type of the elements in the return matrix"
  
  $matrix$`function`$attributes$format_url
  [1] "string"                          "url to the format specification"
  
  $matrix$`function`$attributes$format
  [1] "string"                    "format specification name"
  
  $matrix$`function`$attributes$columns
  $matrix$`function`$attributes$columns[[1]]
  [1] "list"
  
  $matrix$`function`$attributes$columns[[2]]
  $matrix$`function`$attributes$columns[[2]][[1]]
  [1] "object"
  
  $matrix$`function`$attributes$columns[[2]][[2]]
  $matrix$`function`$attributes$columns[[2]][[2]][[1]]
  $matrix$`function`$attributes$columns[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $matrix$`function`$attributes$columns[[2]][[2]][[1]]$id
  [1] "string"                       "unique metagenome identifier"
  
  
  $matrix$`function`$attributes$columns[[2]][[2]][[2]]
  [1] "columns object"
  
  
  
  
  $matrix$`function`$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $matrix$`function`$attributes$shape
  $matrix$`function`$attributes$shape[[1]]
  [1] "list"
  
  $matrix$`function`$attributes$shape[[2]]
  [1] "integer"                                         
  [2] "list of the dimension sizes of the return matrix"
  
  
  $matrix$`function`$attributes$id
  [1] "string"                   "unique object identifier"
  
  $matrix$`function`$attributes$type
  [1] "string"                                                        
  [2] "type of the data in the return table (taxon, function or gene)"
  
  
  
  $matrix$feature
  $matrix$feature$request
  [1] "http://api.metagenomics.anl.gov/matrix/feature"
  
  $matrix$feature$example
  [1] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&source=KEGG&result_type=evalue&length=25"
  [2] "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"                                                    
  
  $matrix$feature$name
  [1] "feature"
  
  $matrix$feature$description
  [1] "Returns a BIOM object."
  
  $matrix$feature$parameters
  $matrix$feature$parameters$body
  named list()
  
  $matrix$feature$parameters$required
  named list()
  
  $matrix$feature$parameters$options
  $matrix$feature$parameters$options$asynchronous
  [1] "boolean"                                                                         
  [2] "if true return process id to query status resource for results, default is false"
  
  $matrix$feature$parameters$options$source
  $matrix$feature$parameters$options$source[[1]]
  [1] "cv"
  
  $matrix$feature$parameters$options$source[[2]]
  $matrix$feature$parameters$options$source[[2]][[1]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[2]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[3]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[4]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[5]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[6]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[7]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[8]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[9]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[10]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[11]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $matrix$feature$parameters$options$source[[2]][[12]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  
  
  $matrix$feature$parameters$options$result_type
  $matrix$feature$parameters$options$result_type[[1]]
  [1] "cv"
  
  $matrix$feature$parameters$options$result_type[[2]]
  $matrix$feature$parameters$options$result_type[[2]][[1]]
  [1] "abundance"                              
  [2] "number of reads with hits in annotation"
  
  $matrix$feature$parameters$options$result_type[[2]][[2]]
  [1] "evalue"                                        
  [2] "average e-value exponent of hits in annotation"
  
  $matrix$feature$parameters$options$result_type[[2]][[3]]
  [1] "identity"                                      
  [2] "average percent identity of hits in annotation"
  
  $matrix$feature$parameters$options$result_type[[2]][[4]]
  [1] "length"                                        
  [2] "average alignment length of hits in annotation"
  
  
  
  $matrix$feature$parameters$options$filter
  [1] "string"                                                                                
  [2] "filter the return results to only include abundances based on genes with this organism"
  
  $matrix$feature$parameters$options$length
  [1] "int"                                                     
  [2] "value for minimum alignment length cutoff: default is 15"
  
  $matrix$feature$parameters$options$evalue
  [1] "int"                                                             
  [2] "negative exponent value for maximum e-value cutoff: default is 5"
  
  $matrix$feature$parameters$options$identity
  [1] "int"                                                       
  [2] "percent value for minimum % identity cutoff: default is 60"
  
  $matrix$feature$parameters$options$hide_annotation
  [1] "boolean"                                                                  
  [2] "if true do not return feature metadata in 'rows' object, default is false"
  
  $matrix$feature$parameters$options$id
  [1] "string"                                             
  [2] "one or more metagenome or project unique identifier"
  
  $matrix$feature$parameters$options$hide_metadata
  [1] "boolean"                                                                        
  [2] "if true do not return metagenome metadata in 'columns' object, default is false"
  
  $matrix$feature$parameters$options$filter_level
  $matrix$feature$parameters$options$filter_level[[1]]
  [1] "cv"
  
  $matrix$feature$parameters$options$filter_level[[2]]
  $matrix$feature$parameters$options$filter_level[[2]][[1]]
  [1] "strain"                          "bottom organism taxanomic level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[2]]
  [1] "species"             "organism type level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[3]]
  [1] "genus"                    "organism taxanomic level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[4]]
  [1] "family"                   "organism taxanomic level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[5]]
  [1] "order"                    "organism taxanomic level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[6]]
  [1] "class"                    "organism taxanomic level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[7]]
  [1] "phylum"                   "organism taxanomic level"
  
  $matrix$feature$parameters$options$filter_level[[2]][[8]]
  [1] "domain"                       "top organism taxanomic level"
  
  
  
  
  
  $matrix$feature$method
  [1] "GET"
  
  $matrix$feature$type
  [1] "synchronous or asynchronous"
  
  $matrix$feature$attributes
  $matrix$feature$attributes$generated_by
  [1] "string"                           "identifier of the data generator"
  
  $matrix$feature$attributes$matrix_type
  [1] "string"                                            
  [2] "type of the data encoding matrix (dense or sparse)"
  
  $matrix$feature$attributes$date
  [1] "date"                               "time the output data was generated"
  
  $matrix$feature$attributes$data
  $matrix$feature$attributes$data[[1]]
  [1] "list"
  
  $matrix$feature$attributes$data[[2]]
  $matrix$feature$attributes$data[[2]][[1]]
  [1] "list"
  
  $matrix$feature$attributes$data[[2]][[2]]
  [1] "float"             "the matrix values"
  
  
  
  $matrix$feature$attributes$rows
  $matrix$feature$attributes$rows[[1]]
  [1] "list"
  
  $matrix$feature$attributes$rows[[2]]
  $matrix$feature$attributes$rows[[2]][[1]]
  [1] "object"
  
  $matrix$feature$attributes$rows[[2]][[2]]
  $matrix$feature$attributes$rows[[2]][[2]][[1]]
  $matrix$feature$attributes$rows[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $matrix$feature$attributes$rows[[2]][[2]][[1]]$id
  [1] "string"                 "unique annotation text"
  
  
  $matrix$feature$attributes$rows[[2]][[2]][[2]]
  [1] "rows object"
  
  
  
  
  $matrix$feature$attributes$matrix_element_value
  [1] "string"                                          
  [2] "result_type of the elements in the return matrix"
  
  $matrix$feature$attributes$matrix_element_type
  [1] "string"                                        
  [2] "data type of the elements in the return matrix"
  
  $matrix$feature$attributes$format_url
  [1] "string"                          "url to the format specification"
  
  $matrix$feature$attributes$format
  [1] "string"                    "format specification name"
  
  $matrix$feature$attributes$columns
  $matrix$feature$attributes$columns[[1]]
  [1] "list"
  
  $matrix$feature$attributes$columns[[2]]
  $matrix$feature$attributes$columns[[2]][[1]]
  [1] "object"
  
  $matrix$feature$attributes$columns[[2]][[2]]
  $matrix$feature$attributes$columns[[2]][[2]][[1]]
  $matrix$feature$attributes$columns[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $matrix$feature$attributes$columns[[2]][[2]][[1]]$id
  [1] "string"                       "unique metagenome identifier"
  
  
  $matrix$feature$attributes$columns[[2]][[2]][[2]]
  [1] "columns object"
  
  
  
  
  $matrix$feature$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $matrix$feature$attributes$shape
  $matrix$feature$attributes$shape[[1]]
  [1] "list"
  
  $matrix$feature$attributes$shape[[2]]
  [1] "integer"                                         
  [2] "list of the dimension sizes of the return matrix"
  
  
  $matrix$feature$attributes$id
  [1] "string"                   "unique object identifier"
  
  $matrix$feature$attributes$type
  [1] "string"                                                        
  [2] "type of the data in the return table (taxon, function or gene)"
  
  
  
  
  $metadata
  $metadata$info
  $metadata$info$parameters
  $metadata$info$parameters$body
  named list()
  
  $metadata$info$parameters$required
  named list()
  
  $metadata$info$parameters$options
  named list()
  
  
  $metadata$info$request
  [1] "http://api.metagenomics.anl.gov/metadata"
  
  $metadata$info$name
  [1] "info"
  
  $metadata$info$type
  [1] "synchronous"
  
  $metadata$info$method
  [1] "GET"
  
  $metadata$info$attributes
  [1] "self"
  
  $metadata$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $metadata$template
  $metadata$template$request
  [1] "http://api.metagenomics.anl.gov/metadata/template"
  
  $metadata$template$example
  [1] "http://api.metagenomics.anl.gov/metadata/template"
  [2] "metadata template"                                
  
  $metadata$template$name
  [1] "template"
  
  $metadata$template$description
  [1] "Returns static template for metadata object relationships and types"
  
  $metadata$template$parameters
  $metadata$template$parameters$body
  named list()
  
  $metadata$template$parameters$required
  named list()
  
  $metadata$template$parameters$options
  named list()
  
  
  $metadata$template$method
  [1] "GET"
  
  $metadata$template$type
  [1] "synchronous"
  
  $metadata$template$attributes
  $metadata$template$attributes$ep
  $metadata$template$attributes$ep[[1]]
  [1] "hash"
  
  $metadata$template$attributes$ep[[2]]
  $metadata$template$attributes$ep[[2]][[1]]
  $metadata$template$attributes$ep[[2]][[1]]$value
  [1] "hash"                              "hash of metadata objects by label"
  
  $metadata$template$attributes$ep[[2]][[1]]$key
  [1] "string"                    "enviromental package type"
  
  
  $metadata$template$attributes$ep[[2]][[2]]
  [1] "eps and their metadata"
  
  
  
  $metadata$template$attributes$project
  $metadata$template$attributes$project[[1]]
  [1] "hash"
  
  $metadata$template$attributes$project[[2]]
  $metadata$template$attributes$project[[2]][[1]]
  $metadata$template$attributes$project[[2]][[1]]$value
  [1] "hash"                              "hash of metadata objects by label"
  
  $metadata$template$attributes$project[[2]][[1]]$key
  [1] "string"       "project type"
  
  
  $metadata$template$attributes$project[[2]][[2]]
  [1] "projects and their metadata"
  
  
  
  $metadata$template$attributes$library
  $metadata$template$attributes$library[[1]]
  [1] "hash"
  
  $metadata$template$attributes$library[[2]]
  $metadata$template$attributes$library[[2]][[1]]
  $metadata$template$attributes$library[[2]][[1]]$value
  [1] "hash"                              "hash of metadata objects by label"
  
  $metadata$template$attributes$library[[2]][[1]]$key
  [1] "string"       "library type"
  
  
  $metadata$template$attributes$library[[2]][[2]]
  [1] "libraries and their metadata"
  
  
  
  $metadata$template$attributes$sample
  $metadata$template$attributes$sample[[1]]
  [1] "hash"
  
  $metadata$template$attributes$sample[[2]]
  $metadata$template$attributes$sample[[2]][[1]]
  $metadata$template$attributes$sample[[2]][[1]]$value
  [1] "hash"                              "hash of metadata objects by label"
  
  $metadata$template$attributes$sample[[2]][[1]]$key
  [1] "string"      "sample type"
  
  
  $metadata$template$attributes$sample[[2]][[2]]
  [1] "samples and their metadata"
  
  
  
  
  
  $metadata$cv
  $metadata$cv$request
  [1] "http://api.metagenomics.anl.gov/metadata/cv"
  
  $metadata$cv$example
  [1] "http://api.metagenomics.anl.gov/metadata/cv?label=country"
  [2] "metadata controlled vocabularies"                         
  
  $metadata$cv$name
  [1] "cv"
  
  $metadata$cv$description
  [1] "Returns static controlled vocabularies used in metadata. By default returns all CVs at latest version. If label and version options used, returns those specific values."
  
  $metadata$cv$parameters
  $metadata$cv$parameters$body
  named list()
  
  $metadata$cv$parameters$options
  $metadata$cv$parameters$options$version
  [1] "string"                                      
  [2] "version of CV select list or ontology to use"
  
  $metadata$cv$parameters$options$label
  [1] "string"         "metadata label"
  
  
  $metadata$cv$parameters$required
  named list()
  
  
  $metadata$cv$method
  [1] "GET"
  
  $metadata$cv$type
  [1] "synchronous"
  
  $metadata$cv$attributes
  $metadata$cv$attributes$ontology
  $metadata$cv$attributes$ontology[[1]]
  [1] "hash"
  
  $metadata$cv$attributes$ontology[[2]]
  $metadata$cv$attributes$ontology[[2]][[1]]
  $metadata$cv$attributes$ontology[[2]][[1]]$value
  $metadata$cv$attributes$ontology[[2]][[1]]$value[[1]]
  [1] "list"
  
  $metadata$cv$attributes$ontology[[2]][[1]]$value[[2]]
  $metadata$cv$attributes$ontology[[2]][[1]]$value[[2]][[1]]
  [1] "list"
  
  $metadata$cv$attributes$ontology[[2]][[1]]$value[[2]][[2]]
  [1] "string"               "ontology term and ID"
  
  
  
  $metadata$cv$attributes$ontology[[2]][[1]]$key
  [1] "string"         "metadata label"
  
  
  $metadata$cv$attributes$ontology[[2]][[2]]
  [1] "list of CV terms for metadata"
  
  
  
  $metadata$cv$attributes$ont_info
  $metadata$cv$attributes$ont_info[[1]]
  [1] "hash"
  
  $metadata$cv$attributes$ont_info[[2]]
  $metadata$cv$attributes$ont_info[[2]][[1]]
  $metadata$cv$attributes$ont_info[[2]][[1]]$value
  $metadata$cv$attributes$ont_info[[2]][[1]]$value[[1]]
  [1] "list"
  
  $metadata$cv$attributes$ont_info[[2]][[1]]$value[[2]]
  [1] "string"              "ontology url and ID"
  
  
  $metadata$cv$attributes$ont_info[[2]][[1]]$key
  [1] "string"         "metadata label"
  
  
  $metadata$cv$attributes$ont_info[[2]][[2]]
  [1] "term IDs for metadata"
  
  
  
  $metadata$cv$attributes$select
  $metadata$cv$attributes$select[[1]]
  [1] "hash"
  
  $metadata$cv$attributes$select[[2]]
  $metadata$cv$attributes$select[[2]][[1]]
  $metadata$cv$attributes$select[[2]][[1]]$value
  $metadata$cv$attributes$select[[2]][[1]]$value[[1]]
  [1] "list"
  
  $metadata$cv$attributes$select[[2]][[1]]$value[[2]]
  [1] "string"  "CV term"
  
  
  $metadata$cv$attributes$select[[2]][[1]]$key
  [1] "string"         "metadata label"
  
  
  $metadata$cv$attributes$select[[2]][[2]]
  [1] "list of CV terms for metadata"
  
  
  
  
  
  $metadata$ontology
  $metadata$ontology$request
  [1] "http://api.metagenomics.anl.gov/metadata/ontology"
  
  $metadata$ontology$example
  [1] "http://api.metagenomics.anl.gov/metadata/ontology?name=biome&version=2013-04-27"
  [2] "metadata ontology lookup"                                                       
  
  $metadata$ontology$name
  [1] "ontology"
  
  $metadata$ontology$description
  [1] "Returns static ontology used in metadata for the given name and version."
  
  $metadata$ontology$parameters
  $metadata$ontology$parameters$body
  named list()
  
  $metadata$ontology$parameters$options
  named list()
  
  $metadata$ontology$parameters$required
  $metadata$ontology$parameters$required$version
  [1] "string"                     "version of ontology to use"
  
  $metadata$ontology$parameters$required$name
  [1] "string"        "ontology name"
  
  
  
  $metadata$ontology$method
  [1] "GET"
  
  $metadata$ontology$type
  [1] "synchronous"
  
  $metadata$ontology$attributes
  $metadata$ontology$attributes$version
  [1] "string"                   "version of this ontology"
  
  $metadata$ontology$attributes$rootNode
  [1] "string"              "ontology ID of root"
  
  $metadata$ontology$attributes$name
  [1] "string"        "ontology name"
  
  $metadata$ontology$attributes$type
  [1] "string"    "this type"
  
  $metadata$ontology$attributes$showRoot
  [1] "boolean"                             "option to show root when displaying"
  
  $metadata$ontology$attributes$nodes
  $metadata$ontology$attributes$nodes[[1]]
  [1] "hash"
  
  $metadata$ontology$attributes$nodes[[2]]
  $metadata$ontology$attributes$nodes[[2]][[1]]
  $metadata$ontology$attributes$nodes[[2]][[1]]$value
  [1] "hash"                                                       
  [2] "hash of information and relationships for given ontology ID"
  
  $metadata$ontology$attributes$nodes[[2]][[1]]$key
  [1] "string"      "ontology ID"
  
  
  $metadata$ontology$attributes$nodes[[2]][[2]]
  [1] "info for ontology ID"
  
  
  
  
  
  $metadata$export
  $metadata$export$request
  [1] "http://api.metagenomics.anl.gov/metadata/export/{ID}"
  
  $metadata$export$example
  [1] "http://api.metagenomics.anl.gov/metadata/export/mgp128"
  [2] "all metadata for project mgp128"                       
  
  $metadata$export$name
  [1] "export"
  
  $metadata$export$description
  [1] "Returns full nested metadata for a project in same format as template, or metadata for a single metagenome."
  
  $metadata$export$parameters
  $metadata$export$parameters$body
  named list()
  
  $metadata$export$parameters$required
  $metadata$export$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $metadata$export$parameters$options
  named list()
  
  
  $metadata$export$method
  [1] "GET"
  
  $metadata$export$type
  [1] "synchronous"
  
  $metadata$export$attributes
  $metadata$export$attributes$sampleNum
  [1] "int"                          "number of samples in project"
  
  $metadata$export$attributes$samples
  $metadata$export$attributes$samples[[1]]
  [1] "list"
  
  $metadata$export$attributes$samples[[2]]
  [1] "object"                                                                       
  [2] "sample object containing sample metadata, sample libraries, sample envPackage"
  
  
  $metadata$export$attributes$name
  [1] "string"                    "human readable identifier"
  
  $metadata$export$attributes$data
  $metadata$export$attributes$data[[1]]
  [1] "hash"
  
  $metadata$export$attributes$data[[2]]
  $metadata$export$attributes$data[[2]][[1]]
  $metadata$export$attributes$data[[2]][[1]]$value
  [1] "object"                   "project metadata objects"
  
  $metadata$export$attributes$data[[2]][[1]]$key
  [1] "string"         "metadata label"
  
  
  $metadata$export$attributes$data[[2]][[2]]
  [1] "hash of metadata by label"
  
  
  
  $metadata$export$attributes$id
  [1] "string"                   "unique object identifier"
  
  
  
  $metadata$validate
  $metadata$validate$request
  [1] "http://api.metagenomics.anl.gov/metadata/validate"
  
  $metadata$validate$example
  [1] "http://api.metagenomics.anl.gov/metadata/validate?category=sample&label=material&value=soil"
  [2] "check if 'soil' is a vaild term for sample material"                                        
  
  $metadata$validate$name
  [1] "validate"
  
  $metadata$validate$description
  [1] "Validate given metadata value"
  
  $metadata$validate$parameters
  $metadata$validate$parameters$body
  named list()
  
  $metadata$validate$parameters$options
  $metadata$validate$parameters$options$group
  $metadata$validate$parameters$options$group[[1]]
  [1] "cv"
  
  $metadata$validate$parameters$options$group[[2]]
  $metadata$validate$parameters$options$group[[2]][[1]]
  [1] "mixs"                                    
  [2] "label is part of MIxS (minimal) metadata"
  
  $metadata$validate$parameters$options$group[[2]][[2]]
  [1] "mims"                                       
  [2] "label is part of MIMS (metagenome) metadata"
  
  $metadata$validate$parameters$options$group[[2]][[3]]
  [1] "migs"                                   
  [2] "label is part of MIGS (genome) metadata"
  
  
  
  $metadata$validate$parameters$options$version
  [1] "string"                                      
  [2] "version of CV select list or ontology to use"
  
  $metadata$validate$parameters$options$value
  [1] "string"         "metadata value"
  
  $metadata$validate$parameters$options$label
  [1] "string"         "metadata label"
  
  $metadata$validate$parameters$options$category
  $metadata$validate$parameters$options$category[[1]]
  [1] "cv"
  
  $metadata$validate$parameters$options$category[[2]]
  $metadata$validate$parameters$options$category[[2]][[1]]
  [1] "project"                           "label belongs to project metadata"
  
  $metadata$validate$parameters$options$category[[2]][[2]]
  [1] "sample"                           "label belongs to sample metadata"
  
  $metadata$validate$parameters$options$category[[2]][[3]]
  [1] "library"                           "label belongs to library metadata"
  
  $metadata$validate$parameters$options$category[[2]][[4]]
  [1] "env_package"                          
  [2] "label belongs to env_package metadata"
  
  
  
  
  $metadata$validate$parameters$required
  named list()
  
  
  $metadata$validate$method
  [1] "GET"
  
  $metadata$validate$type
  [1] "synchronous"
  
  $metadata$validate$attributes
  $metadata$validate$attributes$message
  [1] "string"                   "if not valid, reason why"
  
  $metadata$validate$attributes$is_valid
  [1] "boolean"                                                    
  [2] "the inputed value is valid for the given category and label"
  
  
  
  
  $metagenome
  $metagenome$info
  $metagenome$info$parameters
  $metagenome$info$parameters$body
  named list()
  
  $metagenome$info$parameters$required
  named list()
  
  $metagenome$info$parameters$options
  named list()
  
  
  $metagenome$info$request
  [1] "http://api.metagenomics.anl.gov/metagenome"
  
  $metagenome$info$name
  [1] "info"
  
  $metagenome$info$type
  [1] "synchronous"
  
  $metagenome$info$method
  [1] "GET"
  
  $metagenome$info$attributes
  [1] "self"
  
  $metagenome$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $metagenome$query
  $metagenome$query$request
  [1] "http://api.metagenomics.anl.gov/metagenome"
  
  $metagenome$query$example
  [1] "http://api.metagenomics.anl.gov/metagenome?limit=20&order=name"
  [2] "retrieve the first 20 metagenomes ordered by name"             
  
  $metagenome$query$name
  [1] "query"
  
  $metagenome$query$description
  [1] "Returns a set of data matching the query criteria."
  
  $metagenome$query$parameters
  $metagenome$query$parameters$body
  named list()
  
  $metagenome$query$parameters$required
  named list()
  
  $metagenome$query$parameters$options
  $metagenome$query$parameters$options$verbosity
  $metagenome$query$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $metagenome$query$parameters$options$verbosity[[2]]
  $metagenome$query$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  $metagenome$query$parameters$options$verbosity[[2]][[2]]
  [1] "mixs"                          "returns all GSC MIxS metadata"
  
  $metagenome$query$parameters$options$verbosity[[2]][[3]]
  [1] "metadata"                      "returns minimal with metadata"
  
  $metagenome$query$parameters$options$verbosity[[2]][[4]]
  [1] "stats"                           "returns minimal with statistics"
  
  $metagenome$query$parameters$options$verbosity[[2]][[5]]
  [1] "full"                                "returns all metadata and statistics"
  
  
  
  $metagenome$query$parameters$options$`function`
  [1] "string"                                     
  [2] "search parameter: query string for function"
  
  $metagenome$query$parameters$options$status
  $metagenome$query$parameters$options$status[[1]]
  [1] "cv"
  
  $metagenome$query$parameters$options$status[[2]]
  $metagenome$query$parameters$options$status[[2]][[1]]
  [1] "both"                                                         
  [2] "returns all data (public and private) user has access to view"
  
  $metagenome$query$parameters$options$status[[2]][[2]]
  [1] "public"                  "returns all public data"
  
  $metagenome$query$parameters$options$status[[2]][[3]]
  [1] "private"                                     
  [2] "returns private data user has access to view"
  
  
  
  $metagenome$query$parameters$options$match
  $metagenome$query$parameters$options$match[[1]]
  [1] "cv"
  
  $metagenome$query$parameters$options$match[[2]]
  $metagenome$query$parameters$options$match[[2]][[1]]
  [1] "all"                                                
  [2] "return metagenomes that match all search parameters"
  
  $metagenome$query$parameters$options$match[[2]][[2]]
  [1] "any"                                                
  [2] "return metagenomes that match any search parameters"
  
  
  
  $metagenome$query$parameters$options$direction
  $metagenome$query$parameters$options$direction[[1]]
  [1] "cv"
  
  $metagenome$query$parameters$options$direction[[2]]
  $metagenome$query$parameters$options$direction[[2]][[1]]
  [1] "asc"                     "sort by ascending order"
  
  $metagenome$query$parameters$options$direction[[2]][[2]]
  [1] "desc"                     "sort by descending order"
  
  
  
  $metagenome$query$parameters$options$order
  [1] "string"                                            
  [2] "metagenome object field to sort by (default is id)"
  
  $metagenome$query$parameters$options$metadata
  [1] "string"                                               
  [2] "search parameter: query string for any metadata field"
  
  $metagenome$query$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $metagenome$query$parameters$options$md5
  [1] "string"                                            
  [2] "search parameter: md5 checksum of feature sequence"
  
  $metagenome$query$parameters$options$organism
  [1] "string"                                     
  [2] "search parameter: query string for organism"
  
  $metagenome$query$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $metagenome$query$method
  [1] "GET"
  
  $metagenome$query$type
  [1] "synchronous"
  
  $metagenome$query$attributes
  $metagenome$query$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $metagenome$query$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $metagenome$query$attributes$version
  [1] "integer"               "version of the object"
  
  $metagenome$query$attributes$data
  $metagenome$query$attributes$data[[1]]
  [1] "list"
  
  $metagenome$query$attributes$data[[2]]
  $metagenome$query$attributes$data[[2]][[1]]
  [1] "object"
  
  $metagenome$query$attributes$data[[2]][[2]]
  $metagenome$query$attributes$data[[2]][[2]][[1]]
  $metagenome$query$attributes$data[[2]][[2]][[1]]$PI_firstname
  [1] "string"                              "principal investigator's first name"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$status
  $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[1]]
  [1] "cv"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[2]]
  $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[2]][[1]]
  [1] "public"               "metagenome is public"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[2]][[2]]
  [1] "private"               "metagenome is private"
  
  
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$sequence_type
  [1] "string"          "sequencing type"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$collection_date
  [1] "string"                "date sample collected"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$feature
  [1] "string"                           "environmental feature, EnvO term"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$PI_lastname
  [1] "string"                             "principal investigator's last name"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$latitude
  [1] "string"                      "latitude where sample taken"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$biome
  [1] "string"                         "environmental biome, EnvO term"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$id
  [1] "string"                       "unique metagenome identifier"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$project_name
  [1] "string"                               
  [2] "name of project containing metagenome"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$project_id
  [1] "string"                              "id of project containing metagenome"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$country
  [1] "string"                     "country where sample taken"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$env_package_type
  [1] "string"                                  
  [2] "enviromental package of sample, GSC term"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$longitude
  [1] "string"                       "longitude where sample taken"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$location
  [1] "string"                      "location where sample taken"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$name
  [1] "string"             "name of metagenome"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$seq_method
  [1] "string"            "sequencing method"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$created
  [1] "date"                                 
  [2] "time the metagenome was first created"
  
  $metagenome$query$attributes$data[[2]][[2]][[1]]$material
  [1] "string"                            "environmental material, EnvO term"
  
  
  $metagenome$query$attributes$data[[2]][[2]][[2]]
  [1] "metagenome object"
  
  
  
  
  $metagenome$query$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  $metagenome$query$attributes$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $metagenome$query$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $metagenome$query$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $metagenome$query$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  
  
  $metagenome$instance
  $metagenome$instance$request
  [1] "http://api.metagenomics.anl.gov/metagenome/{ID}"
  
  $metagenome$instance$example
  [1] "http://api.metagenomics.anl.gov/metagenome/mgm4447943.3?verbosity=metadata"
  [2] "retrieve all metadata for metagenome mgm4447943.3"                         
  
  $metagenome$instance$name
  [1] "instance"
  
  $metagenome$instance$description
  [1] "Returns a single data object."
  
  $metagenome$instance$parameters
  $metagenome$instance$parameters$body
  named list()
  
  $metagenome$instance$parameters$required
  $metagenome$instance$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $metagenome$instance$parameters$options
  $metagenome$instance$parameters$options$verbosity
  $metagenome$instance$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $metagenome$instance$parameters$options$verbosity[[2]]
  $metagenome$instance$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  $metagenome$instance$parameters$options$verbosity[[2]][[2]]
  [1] "metadata"                      "returns minimal with metadata"
  
  $metagenome$instance$parameters$options$verbosity[[2]][[3]]
  [1] "stats"                           "returns minimal with statistics"
  
  $metagenome$instance$parameters$options$verbosity[[2]][[4]]
  [1] "full"                                "returns all metadata and statistics"
  
  
  
  
  
  $metagenome$instance$method
  [1] "GET"
  
  $metagenome$instance$type
  [1] "synchronous"
  
  $metagenome$instance$attributes
  $metagenome$instance$attributes$statistics
  [1] "hash"                                 
  [2] "key value pairs describing statistics"
  
  $metagenome$instance$attributes$status
  $metagenome$instance$attributes$status[[1]]
  [1] "cv"
  
  $metagenome$instance$attributes$status[[2]]
  $metagenome$instance$attributes$status[[2]][[1]]
  [1] "public"               "metagenome is public"
  
  $metagenome$instance$attributes$status[[2]][[2]]
  [1] "private"               "metagenome is private"
  
  
  
  $metagenome$instance$attributes$version
  [1] "integer"                   "version of the metagenome"
  
  $metagenome$instance$attributes$project
  [1] "reference project"               "reference to the project object"
  
  $metagenome$instance$attributes$name
  [1] "string"             "name of metagenome"
  
  $metagenome$instance$attributes$sequence_type
  [1] "string"          "sequencing type"
  
  $metagenome$instance$attributes$library
  [1] "reference library"                      
  [2] "reference to the related library object"
  
  $metagenome$instance$attributes$created
  [1] "date"                                 
  [2] "time the metagenome was first created"
  
  $metagenome$instance$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $metagenome$instance$attributes$id
  [1] "string"                       "unique metagenome identifier"
  
  $metagenome$instance$attributes$sample
  [1] "reference sample"                      
  [2] "reference to the related sample object"
  
  $metagenome$instance$attributes$metadata
  [1] "hash"                                   
  [2] "key value pairs describing all metadata"
  
  $metagenome$instance$attributes$mixs
  [1] "hash"                                    
  [2] "key value pairs describing MIxS metadata"
  
  
  
  
  $profile
  $profile$info
  $profile$info$parameters
  $profile$info$parameters$body
  named list()
  
  $profile$info$parameters$required
  named list()
  
  $profile$info$parameters$options
  named list()
  
  
  $profile$info$request
  [1] "http://api.metagenomics.anl.gov/profile"
  
  $profile$info$name
  [1] "info"
  
  $profile$info$type
  [1] "synchronous"
  
  $profile$info$method
  [1] "GET"
  
  $profile$info$attributes
  [1] "self"
  
  $profile$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $profile$instance
  $profile$instance$parameters
  $profile$instance$parameters$body
  named list()
  
  $profile$instance$parameters$required
  $profile$instance$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $profile$instance$parameters$options
  $profile$instance$parameters$options$source
  $profile$instance$parameters$options$source[[1]]
  [1] "cv"
  
  $profile$instance$parameters$options$source[[2]]
  $profile$instance$parameters$options$source[[2]][[1]]
  [1] "M5NR"
  
  $profile$instance$parameters$options$source[[2]][[2]]
  [1] "RefSeq"                                            
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[3]]
  [1] "GenBank"                                           
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[4]]
  [1] "IMG"                                               
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[5]]
  [1] "SEED"                                              
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[6]]
  [1] "TrEMBL"                                            
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[7]]
  [1] "SwissProt"                                         
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[8]]
  [1] "PATRIC"                                            
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[9]]
  [1] "KEGG"                                              
  [2] "protein database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[10]]
  [1] "M5RNA"
  
  $profile$instance$parameters$options$source[[2]][[11]]
  [1] "RDP"                                           
  [2] "RNA database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[12]]
  [1] "Greengenes"                                    
  [2] "RNA database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[13]]
  [1] "LSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[14]]
  [1] "SSU"                                           
  [2] "RNA database, type organism, function, feature"
  
  $profile$instance$parameters$options$source[[2]][[15]]
  [1] "Subsystems"                           
  [2] "ontology database, type ontology only"
  
  $profile$instance$parameters$options$source[[2]][[16]]
  [1] "NOG"                                  
  [2] "ontology database, type ontology only"
  
  $profile$instance$parameters$options$source[[2]][[17]]
  [1] "COG"                                  
  [2] "ontology database, type ontology only"
  
  $profile$instance$parameters$options$source[[2]][[18]]
  [1] "KO"                                   
  [2] "ontology database, type ontology only"
  
  
  
  $profile$instance$parameters$options$length
  [1] "int"                                                     
  [2] "value for minimum alignment length cutoff: default is 15"
  
  $profile$instance$parameters$options$identity
  [1] "int"                                                       
  [2] "percent value for minimum % identity cutoff: default is 60"
  
  $profile$instance$parameters$options$evalue
  [1] "int"                                                             
  [2] "negative exponent value for maximum e-value cutoff: default is 5"
  
  $profile$instance$parameters$options$type
  $profile$instance$parameters$options$type[[1]]
  [1] "cv"
  
  $profile$instance$parameters$options$type[[2]]
  $profile$instance$parameters$options$type[[2]][[1]]
  [1] "organism"             "return organism data"
  
  $profile$instance$parameters$options$type[[2]][[2]]
  [1] "function"               "return functional data"
  
  $profile$instance$parameters$options$type[[2]][[3]]
  [1] "feature"             "return feature data"
  
  
  
  $profile$instance$parameters$options$hit_type
  $profile$instance$parameters$options$hit_type[[1]]
  [1] "cv"
  
  $profile$instance$parameters$options$hit_type[[2]]
  $profile$instance$parameters$options$hit_type[[2]][[1]]
  [1] "all"                                                                        
  [2] "returns results based on all organisms that map to top hit per read-feature"
  
  $profile$instance$parameters$options$hit_type[[2]][[2]]
  [1] "single"                                                                 
  [2] "returns results based on a single organism for top hit per read-feature"
  
  $profile$instance$parameters$options$hit_type[[2]][[3]]
  [1] "lca"                                                                                                                        
  [2] "returns results based on the Least Common Ancestor for all organisms (M5NR+M5RNA only) that map to hits from a read-feature"
  
  
  
  
  
  $profile$instance$name
  [1] "instance"
  
  $profile$instance$type
  [1] "synchronous"
  
  $profile$instance$method
  [1] "GET"
  
  $profile$instance$attributes
  $profile$instance$attributes$generated_by
  [1] "string"                           "identifier of the data generator"
  
  $profile$instance$attributes$matrix_type
  [1] "string"                                            
  [2] "type of the data encoding matrix (dense or sparse)"
  
  $profile$instance$attributes$date
  [1] "date"                               "time the output data was generated"
  
  $profile$instance$attributes$data
  $profile$instance$attributes$data[[1]]
  [1] "list"
  
  $profile$instance$attributes$data[[2]]
  $profile$instance$attributes$data[[2]][[1]]
  [1] "list"
  
  $profile$instance$attributes$data[[2]][[2]]
  [1] "float"             "the matrix values"
  
  
  
  $profile$instance$attributes$rows
  $profile$instance$attributes$rows[[1]]
  [1] "list"
  
  $profile$instance$attributes$rows[[2]]
  $profile$instance$attributes$rows[[2]][[1]]
  [1] "object"
  
  $profile$instance$attributes$rows[[2]][[2]]
  $profile$instance$attributes$rows[[2]][[2]][[1]]
  $profile$instance$attributes$rows[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $profile$instance$attributes$rows[[2]][[2]][[1]]$id
  [1] "string"            "unique identifier"
  
  
  $profile$instance$attributes$rows[[2]][[2]][[2]]
  [1] "rows object"
  
  
  
  
  $profile$instance$attributes$matrix_element_type
  [1] "string"                                        
  [2] "data type of the elements in the return matrix"
  
  $profile$instance$attributes$format_url
  [1] "string"                          "url to the format specification"
  
  $profile$instance$attributes$format
  [1] "string"                    "format specification name"
  
  $profile$instance$attributes$columns
  $profile$instance$attributes$columns[[1]]
  [1] "list"
  
  $profile$instance$attributes$columns[[2]]
  $profile$instance$attributes$columns[[2]][[1]]
  [1] "object"
  
  $profile$instance$attributes$columns[[2]][[2]]
  $profile$instance$attributes$columns[[2]][[2]][[1]]
  $profile$instance$attributes$columns[[2]][[2]][[1]]$metadata
  [1] "hash"                                     
  [2] "list of metadata, contains the metagenome"
  
  $profile$instance$attributes$columns[[2]][[2]][[1]]$id
  [1] "string"            "unique identifier"
  
  
  $profile$instance$attributes$columns[[2]][[2]][[2]]
  [1] "columns object"
  
  
  
  
  $profile$instance$attributes$id
  [1] "string"                   "unique object identifier"
  
  $profile$instance$attributes$type
  [1] "string"                                                        
  [2] "type of the data in the return table (taxon, function or gene)"
  
  $profile$instance$attributes$shape
  $profile$instance$attributes$shape[[1]]
  [1] "list"
  
  $profile$instance$attributes$shape[[2]]
  [1] "integer"                                         
  [2] "list of the dimension sizes of the return matrix"
  
  
  
  $profile$instance$description
  [1] "Returns a single data object in BIOM format"
  
  
  
  $project
  $project$info
  $project$info$parameters
  $project$info$parameters$body
  named list()
  
  $project$info$parameters$required
  named list()
  
  $project$info$parameters$options
  named list()
  
  
  $project$info$request
  [1] "http://api.metagenomics.anl.gov/project"
  
  $project$info$name
  [1] "info"
  
  $project$info$type
  [1] "synchronous"
  
  $project$info$method
  [1] "GET"
  
  $project$info$attributes
  [1] "self"
  
  $project$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $project$query
  $project$query$request
  [1] "http://api.metagenomics.anl.gov/project"
  
  $project$query$example
  [1] "http://api.metagenomics.anl.gov/project?limit=20&order=name"
  [2] "retrieve the first 20 projects ordered by name"             
  
  $project$query$name
  [1] "query"
  
  $project$query$description
  [1] "Returns a set of data matching the query criteria."
  
  $project$query$parameters
  $project$query$parameters$body
  named list()
  
  $project$query$parameters$required
  named list()
  
  $project$query$parameters$options
  $project$query$parameters$options$verbosity
  $project$query$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $project$query$parameters$options$verbosity[[2]]
  $project$query$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  $project$query$parameters$options$verbosity[[2]][[2]]
  [1] "verbose"              "returns all metadata"
  
  $project$query$parameters$options$verbosity[[2]][[3]]
  [1] "full"                                "returns all metadata and references"
  
  
  
  $project$query$parameters$options$order
  $project$query$parameters$options$order[[1]]
  [1] "cv"
  
  $project$query$parameters$options$order[[2]]
  $project$query$parameters$options$order[[2]][[1]]
  [1] "id"                                "return data objects ordered by id"
  
  $project$query$parameters$options$order[[2]][[2]]
  [1] "name"                                "return data objects ordered by name"
  
  
  
  $project$query$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $project$query$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $project$query$method
  [1] "GET"
  
  $project$query$type
  [1] "synchronous"
  
  $project$query$attributes
  $project$query$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $project$query$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $project$query$attributes$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $project$query$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $project$query$attributes$data
  $project$query$attributes$data[[1]]
  [1] "list"
  
  $project$query$attributes$data[[2]]
  $project$query$attributes$data[[2]][[1]]
  [1] "object"
  
  $project$query$attributes$data[[2]][[2]]
  $project$query$attributes$data[[2]][[2]][[1]]
  $project$query$attributes$data[[2]][[2]][[1]]$status
  $project$query$attributes$data[[2]][[2]][[1]]$status[[1]]
  [1] "cv"
  
  $project$query$attributes$data[[2]][[2]][[1]]$status[[2]]
  $project$query$attributes$data[[2]][[2]][[1]]$status[[2]][[1]]
  [1] "public"           "object is public"
  
  $project$query$attributes$data[[2]][[2]][[1]]$status[[2]][[2]]
  [1] "private"           "object is private"
  
  
  
  $project$query$attributes$data[[2]][[2]][[1]]$version
  [1] "integer"               "version of the object"
  
  $project$query$attributes$data[[2]][[2]][[1]]$name
  [1] "string"                    "human readable identifier"
  
  $project$query$attributes$data[[2]][[2]][[1]]$description
  [1] "string"                                           
  [2] "a short, comprehensive description of the project"
  
  $project$query$attributes$data[[2]][[2]][[1]]$metagenomes
  $project$query$attributes$data[[2]][[2]][[1]]$metagenomes[[1]]
  [1] "list"
  
  $project$query$attributes$data[[2]][[2]][[1]]$metagenomes[[2]]
  [1] "reference metagenome"                                  
  [2] "a list of references to the related metagenome objects"
  
  
  $project$query$attributes$data[[2]][[2]][[1]]$libraries
  $project$query$attributes$data[[2]][[2]][[1]]$libraries[[1]]
  [1] "list"
  
  $project$query$attributes$data[[2]][[2]][[1]]$libraries[[2]]
  [1] "reference library"                                  
  [2] "a list of references to the related library objects"
  
  
  $project$query$attributes$data[[2]][[2]][[1]]$created
  [1] "date"                              "time the object was first created"
  
  $project$query$attributes$data[[2]][[2]][[1]]$samples
  $project$query$attributes$data[[2]][[2]][[1]]$samples[[1]]
  [1] "list"
  
  $project$query$attributes$data[[2]][[2]][[1]]$samples[[2]]
  [1] "reference sample"                                  
  [2] "a list of references to the related sample objects"
  
  
  $project$query$attributes$data[[2]][[2]][[1]]$funding_source
  [1] "string"                                                    
  [2] "the official name of the source of funding of this project"
  
  $project$query$attributes$data[[2]][[2]][[1]]$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $project$query$attributes$data[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $project$query$attributes$data[[2]][[2]][[1]]$id
  [1] "string"                   "unique object identifier"
  
  $project$query$attributes$data[[2]][[2]][[1]]$pi
  [1] "string"                                                              
  [2] "the first and last name of the principal investigator of the project"
  
  
  $project$query$attributes$data[[2]][[2]][[2]]
  [1] "list of the project objects"
  
  
  
  
  $project$query$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  $project$query$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  
  
  $project$instance
  $project$instance$request
  [1] "http://api.metagenomics.anl.gov/project/{ID}"
  
  $project$instance$example
  [1] "http://api.metagenomics.anl.gov/project/mgp128?verbosity=full"
  [2] "retrieve all data for project mgp128"                         
  
  $project$instance$name
  [1] "instance"
  
  $project$instance$description
  [1] "Returns a single data object."
  
  $project$instance$parameters
  $project$instance$parameters$body
  named list()
  
  $project$instance$parameters$required
  $project$instance$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $project$instance$parameters$options
  $project$instance$parameters$options$verbosity
  $project$instance$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $project$instance$parameters$options$verbosity[[2]]
  $project$instance$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  $project$instance$parameters$options$verbosity[[2]][[2]]
  [1] "verbose"              "returns all metadata"
  
  $project$instance$parameters$options$verbosity[[2]][[3]]
  [1] "full"                                "returns all metadata and references"
  
  
  
  
  
  $project$instance$method
  [1] "GET"
  
  $project$instance$type
  [1] "synchronous"
  
  $project$instance$attributes
  $project$instance$attributes$status
  $project$instance$attributes$status[[1]]
  [1] "cv"
  
  $project$instance$attributes$status[[2]]
  $project$instance$attributes$status[[2]][[1]]
  [1] "public"           "object is public"
  
  $project$instance$attributes$status[[2]][[2]]
  [1] "private"           "object is private"
  
  
  
  $project$instance$attributes$version
  [1] "integer"               "version of the object"
  
  $project$instance$attributes$name
  [1] "string"                    "human readable identifier"
  
  $project$instance$attributes$description
  [1] "string"                                           
  [2] "a short, comprehensive description of the project"
  
  $project$instance$attributes$metagenomes
  $project$instance$attributes$metagenomes[[1]]
  [1] "list"
  
  $project$instance$attributes$metagenomes[[2]]
  [1] "reference metagenome"                                  
  [2] "a list of references to the related metagenome objects"
  
  
  $project$instance$attributes$libraries
  $project$instance$attributes$libraries[[1]]
  [1] "list"
  
  $project$instance$attributes$libraries[[2]]
  [1] "reference library"                                  
  [2] "a list of references to the related library objects"
  
  
  $project$instance$attributes$created
  [1] "date"                              "time the object was first created"
  
  $project$instance$attributes$samples
  $project$instance$attributes$samples[[1]]
  [1] "list"
  
  $project$instance$attributes$samples[[2]]
  [1] "reference sample"                                  
  [2] "a list of references to the related sample objects"
  
  
  $project$instance$attributes$funding_source
  [1] "string"                                                    
  [2] "the official name of the source of funding of this project"
  
  $project$instance$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $project$instance$attributes$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  $project$instance$attributes$id
  [1] "string"                   "unique object identifier"
  
  $project$instance$attributes$pi
  [1] "string"                                                              
  [2] "the first and last name of the principal investigator of the project"
  
  
  
  
  $sample
  $sample$info
  $sample$info$parameters
  $sample$info$parameters$body
  named list()
  
  $sample$info$parameters$required
  named list()
  
  $sample$info$parameters$options
  named list()
  
  
  $sample$info$request
  [1] "http://api.metagenomics.anl.gov/sample"
  
  $sample$info$name
  [1] "info"
  
  $sample$info$type
  [1] "synchronous"
  
  $sample$info$method
  [1] "GET"
  
  $sample$info$attributes
  [1] "self"
  
  $sample$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $sample$query
  $sample$query$request
  [1] "http://api.metagenomics.anl.gov/sample"
  
  $sample$query$example
  [1] "http://api.metagenomics.anl.gov/sample?limit=20&order=name"
  [2] "retrieve the first 20 samples ordered by name"             
  
  $sample$query$name
  [1] "query"
  
  $sample$query$description
  [1] "Returns a set of data matching the query criteria."
  
  $sample$query$parameters
  $sample$query$parameters$body
  named list()
  
  $sample$query$parameters$required
  named list()
  
  $sample$query$parameters$options
  $sample$query$parameters$options$order
  $sample$query$parameters$options$order[[1]]
  [1] "cv"
  
  $sample$query$parameters$options$order[[2]]
  $sample$query$parameters$options$order[[2]][[1]]
  [1] "id"                                "return data objects ordered by id"
  
  $sample$query$parameters$options$order[[2]][[2]]
  [1] "name"                                "return data objects ordered by name"
  
  
  
  $sample$query$parameters$options$limit
  [1] "integer"                           "maximum number of items requested"
  
  $sample$query$parameters$options$offset
  [1] "integer"                                                 
  [2] "zero based index of the first data object to be returned"
  
  
  
  $sample$query$method
  [1] "GET"
  
  $sample$query$type
  [1] "synchronous"
  
  $sample$query$attributes
  $sample$query$attributes$`next`
  [1] "uri"                                                      
  [2] "link to the previous set or null if this is the first set"
  
  $sample$query$attributes$prev
  [1] "uri"                                                 
  [2] "link to the next set or null if this is the last set"
  
  $sample$query$attributes$order
  [1] "string"                                               
  [2] "name of the attribute the returned data is ordered by"
  
  $sample$query$attributes$limit
  [1] "integer"                                             
  [2] "maximum number of data items returned, default is 10"
  
  $sample$query$attributes$data
  $sample$query$attributes$data[[1]]
  [1] "list"
  
  $sample$query$attributes$data[[2]]
  $sample$query$attributes$data[[2]][[1]]
  [1] "object"
  
  $sample$query$attributes$data[[2]][[2]]
  $sample$query$attributes$data[[2]][[2]][[1]]
  $sample$query$attributes$data[[2]][[2]][[1]]$version
  [1] "integer"               "version of the object"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$project
  [1] "reference project"                      
  [2] "reference to the project of this sample"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$name
  [1] "string"                    "human readable identifier"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$metagenomes
  $sample$query$attributes$data[[2]][[2]][[1]]$metagenomes[[1]]
  [1] "list"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$metagenomes[[2]]
  [1] "reference metagenome"                                  
  [2] "a list of references to the related metagenome objects"
  
  
  $sample$query$attributes$data[[2]][[2]][[1]]$libraries
  $sample$query$attributes$data[[2]][[2]][[1]]$libraries[[1]]
  [1] "list"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$libraries[[2]]
  [1] "reference library"                                  
  [2] "a list of references to the related library objects"
  
  
  $sample$query$attributes$data[[2]][[2]][[1]]$created
  [1] "date"                              "time the object was first created"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[1]]
  [1] "object"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]]
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$created
  [1] "date"          "creation date"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$name
  [1] "string"              "name of the package"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$id
  [1] "string"                    "unique package identifier"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$type
  [1] "string"       "package type"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  
  $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[2]]
  [1] "environmental package object"
  
  
  
  $sample$query$attributes$data[[2]][[2]][[1]]$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$id
  [1] "string"                   "unique object identifier"
  
  $sample$query$attributes$data[[2]][[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  
  $sample$query$attributes$data[[2]][[2]][[2]]
  [1] "list of sample objects"
  
  
  
  
  $sample$query$attributes$offset
  [1] "integer"                                         
  [2] "zero based index of the first returned data item"
  
  $sample$query$attributes$total_count
  [1] "integer"                             
  [2] "total number of available data items"
  
  
  
  $sample$instance
  $sample$instance$request
  [1] "http://api.metagenomics.anl.gov/sample/{ID}"
  
  $sample$instance$example
  [1] "http://api.metagenomics.anl.gov/sample/mgs25823?verbosity=full"
  [2] "retrieve all data for sample mgs25823"                         
  
  $sample$instance$name
  [1] "instance"
  
  $sample$instance$description
  [1] "Returns a single data object."
  
  $sample$instance$parameters
  $sample$instance$parameters$body
  named list()
  
  $sample$instance$parameters$required
  $sample$instance$parameters$required$id
  [1] "string"                   "unique object identifier"
  
  
  $sample$instance$parameters$options
  $sample$instance$parameters$options$verbosity
  $sample$instance$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $sample$instance$parameters$options$verbosity[[2]]
  $sample$instance$parameters$options$verbosity[[2]][[1]]
  [1] "minimal"                          "returns only minimal information"
  
  $sample$instance$parameters$options$verbosity[[2]][[2]]
  [1] "verbose"              "returns all metadata"
  
  $sample$instance$parameters$options$verbosity[[2]][[3]]
  [1] "full"                                "returns all metadata and references"
  
  
  
  
  
  $sample$instance$method
  [1] "GET"
  
  $sample$instance$type
  [1] "synchronous"
  
  $sample$instance$attributes
  $sample$instance$attributes$version
  [1] "integer"               "version of the object"
  
  $sample$instance$attributes$project
  [1] "reference project"                      
  [2] "reference to the project of this sample"
  
  $sample$instance$attributes$name
  [1] "string"                    "human readable identifier"
  
  $sample$instance$attributes$metagenomes
  $sample$instance$attributes$metagenomes[[1]]
  [1] "list"
  
  $sample$instance$attributes$metagenomes[[2]]
  [1] "reference metagenome"                                  
  [2] "a list of references to the related metagenome objects"
  
  
  $sample$instance$attributes$libraries
  $sample$instance$attributes$libraries[[1]]
  [1] "list"
  
  $sample$instance$attributes$libraries[[2]]
  [1] "reference library"                                  
  [2] "a list of references to the related library objects"
  
  
  $sample$instance$attributes$created
  [1] "date"                              "time the object was first created"
  
  $sample$instance$attributes$env_package
  $sample$instance$attributes$env_package[[1]]
  [1] "object"
  
  $sample$instance$attributes$env_package[[2]]
  $sample$instance$attributes$env_package[[2]][[1]]
  $sample$instance$attributes$env_package[[2]][[1]]$created
  [1] "date"          "creation date"
  
  $sample$instance$attributes$env_package[[2]][[1]]$name
  [1] "string"              "name of the package"
  
  $sample$instance$attributes$env_package[[2]][[1]]$id
  [1] "string"                    "unique package identifier"
  
  $sample$instance$attributes$env_package[[2]][[1]]$type
  [1] "string"       "package type"
  
  $sample$instance$attributes$env_package[[2]][[1]]$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  
  $sample$instance$attributes$env_package[[2]][[2]]
  [1] "environmental package object"
  
  
  
  $sample$instance$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $sample$instance$attributes$id
  [1] "string"                   "unique object identifier"
  
  $sample$instance$attributes$metadata
  [1] "hash"                                "key value pairs describing metadata"
  
  
  
  
  $server
  $server$info
  $server$info$parameters
  $server$info$parameters$body
  named list()
  
  $server$info$parameters$required
  named list()
  
  $server$info$parameters$options
  named list()
  
  
  $server$info$request
  [1] "http://api.metagenomics.anl.gov/server"
  
  $server$info$name
  [1] "info"
  
  $server$info$type
  [1] "synchronous"
  
  $server$info$method
  [1] "GET"
  
  $server$info$attributes
  [1] "self"
  
  $server$info$description
  [1] "Returns the server information."
  
  
  $server$instance
  $server$instance$request
  [1] "http://api.metagenomics.anl.gov/server/{ID}"
  
  $server$instance$example
  [1] "curl -X GET \"http://api.metagenomics.anl.gov/server/MG-RAST\""
  [2] "info for the MG-RAST server"                                   
  
  $server$instance$name
  [1] "instance"
  
  $server$instance$description
  [1] "Returns a single user object."
  
  $server$instance$parameters
  $server$instance$parameters$body
  named list()
  
  $server$instance$parameters$required
  $server$instance$parameters$required$id
  [1] "string"           "unique server ID"
  
  
  $server$instance$parameters$options
  named list()
  
  
  $server$instance$method
  [1] "GET"
  
  $server$instance$type
  [1] "synchronous"
  
  $server$instance$attributes
  $server$instance$attributes$info
  [1] "string"                                    
  [2] "informational text, i.e. downtime warnings"
  
  $server$instance$attributes$basepairs
  [1] "integer"                   "total number of basepairs"
  
  $server$instance$attributes$status
  [1] "string"               "status of the server"
  
  $server$instance$attributes$version
  [1] "string"                       "version number of the server"
  
  $server$instance$attributes$url
  [1] "uri"                                      
  [2] "resource location of this object instance"
  
  $server$instance$attributes$id
  [1] "string"                           "unique identifier of this server"
  
  $server$instance$attributes$public_metagenomes
  [1] "integer"                            "total number of public metagenomes"
  
  $server$instance$attributes$metagenomes
  [1] "integer"                     "total number of metagenomes"
  
  $server$instance$attributes$sequences
  [1] "integer"                   "total number of sequences"
  
  
  
  
  $validation
  $validation$info
  $validation$info$parameters
  $validation$info$parameters$body
  named list()
  
  $validation$info$parameters$required
  named list()
  
  $validation$info$parameters$options
  named list()
  
  
  $validation$info$request
  [1] "http://api.metagenomics.anl.gov/validation"
  
  $validation$info$name
  [1] "info"
  
  $validation$info$type
  [1] "synchronous"
  
  $validation$info$method
  [1] "GET"
  
  $validation$info$attributes
  [1] "self"
  
  $validation$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $validation$template
  $validation$template$request
  [1] "http://api.metagenomics.anl.gov/validation/template/{ID}"
  
  $validation$template$example
  [1] "http://api.metagenomics.anl.gov/validation/template/"
  [2] "validate the communities metagenomics template"      
  
  $validation$template$name
  [1] "template"
  
  $validation$template$description
  [1] "Checks if the referenced JSON structure is a valid template"
  
  $validation$template$parameters
  $validation$template$parameters$body
  named list()
  
  $validation$template$parameters$required
  $validation$template$parameters$required$id
  [1] "string"            "SHOCK template id"
  
  
  $validation$template$parameters$options
  named list()
  
  
  $validation$template$method
  [1] "GET"
  
  $validation$template$type
  [1] "synchronous"
  
  $validation$template$attributes
  $validation$template$attributes$error
  $validation$template$attributes$error[[1]]
  [1] "array"
  
  $validation$template$attributes$error[[2]]
  [1] "string"                   "array of invalid entries"
  
  
  $validation$template$attributes$valid
  [1] "boolean"                                                         
  [2] "boolean indicating whether the examined template is valid or not"
  
  
  
  $validation$data
  $validation$data$request
  [1] "http://api.metagenomics.anl.gov/validation/data/{ID}"
  
  $validation$data$example
  [1] "http://api.metagenomics.anl.gov/validation/data/?template="                     
  [2] "validate a JSON data structure against the MG-RAST metagenome metadata template"
  
  $validation$data$name
  [1] "data"
  
  $validation$data$description
  [1] "Returns a single data object."
  
  $validation$data$parameters
  $validation$data$parameters$body
  named list()
  
  $validation$data$parameters$required
  $validation$data$parameters$required$id
  [1] "string"        "SHOCK data id"
  
  
  $validation$data$parameters$options
  $validation$data$parameters$options$template
  [1] "string"                                                            
  [2] "SHOCK template id, default is MG-RAST metagenome metadata template"
  
  
  
  $validation$data$method
  [1] "GET"
  
  $validation$data$type
  [1] "synchronous"
  
  $validation$data$attributes
  $validation$data$attributes$error
  $validation$data$attributes$error[[1]]
  [1] "array"
  
  $validation$data$attributes$error[[2]]
  [1] "string"                   "array of invalid entries"
  
  
  $validation$data$attributes$valid
  [1] "boolean"                                                         
  [2] "boolean indicating whether the examined template is valid or not"
  
  
  
  
  $status
  $status$info
  $status$info$parameters
  $status$info$parameters$body
  named list()
  
  $status$info$parameters$required
  named list()
  
  $status$info$parameters$options
  named list()
  
  
  $status$info$request
  [1] "http://api.metagenomics.anl.gov/status"
  
  $status$info$name
  [1] "info"
  
  $status$info$type
  [1] "synchronous"
  
  $status$info$method
  [1] "GET"
  
  $status$info$attributes
  [1] "self"
  
  $status$info$description
  [1] "Returns description of parameters and attributes."
  
  
  $status$instance
  $status$instance$request
  [1] "http://api.metagenomics.anl.gov/status/{TOKEN}"
  
  $status$instance$example
  [1] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/status/12345\""
  [2] "data for asynchronous call with ID 12345"                                          
  
  $status$instance$name
  [1] "instance"
  
  $status$instance$description
  [1] "Returns a single data object."
  
  $status$instance$parameters
  $status$instance$parameters$body
  named list()
  
  $status$instance$parameters$required
  $status$instance$parameters$required$id
  [1] "string"            "unique process id"
  
  
  $status$instance$parameters$options
  $status$instance$parameters$options$verbosity
  $status$instance$parameters$options$verbosity[[1]]
  [1] "cv"
  
  $status$instance$parameters$options$verbosity[[2]]
  $status$instance$parameters$options$verbosity[[2]][[1]]
  [1] "full"                           "returns all connected metadata"
  
  $status$instance$parameters$options$verbosity[[2]][[2]]
  [1] "minimal"                          "returns only minimal information"
  
  
  
  
  
  $status$instance$method
  [1] "GET"
  
  $status$instance$type
  [1] "synchronous"
  
  $status$instance$attributes
  $status$instance$attributes$status
  $status$instance$attributes$status[[1]]
  [1] "string"
  
  $status$instance$attributes$status[[2]]
  [1] "cv"
  
  $status$instance$attributes$status[[3]]
  $status$instance$attributes$status[[3]][[1]]
  [1] "processing"                 "process is still computing"
  
  $status$instance$attributes$status[[3]][[2]]
  [1] "done"                      "process is done computing"
  
  
  
  $status$instance$attributes$url
  [1] "url"                                      
  [2] "resource location of this object instance"
  
  $status$instance$attributes$data
  [1] "hash"                                                                   
  [2] "if status is done, data holds the result, otherwise data is not present"
  
  $status$instance$attributes$id
  [1] "integer"    "process id"
  
  
  
  
  > API <- get ("API", envir=.MGRAST)
  > 
  > #-----------------------------------------------------------------------------
  > #  test docs
  > #-----------------------------------------------------------------------------
  > 
  > doc.MGRAST()
  List of 15
   $ annotation:List of 3
   $ compute   :List of 2
   $ download  :List of 3
   $ inbox     :List of 2
   $ library   :List of 3
   $ m5nr      :List of 10
   $ matrix    :List of 4
   $ metadata  :List of 6
   $ metagenome:List of 3
   $ profile   :List of 2
   $ project   :List of 3
   $ sample    :List of 3
   $ server    :List of 2
   $ validation:List of 3
   $ status    :List of 2
  > doc.MGRAST(2)
  List of 15
   $ annotation:List of 3
    ..$ info      :List of 7
    ..$ sequence  :List of 8
    ..$ similarity:List of 8
   $ compute   :List of 2
    ..$ info          :List of 7
    ..$ alphadiversity:List of 8
   $ download  :List of 3
    ..$ info    :List of 7
    ..$ instance:List of 8
    ..$ setlist :List of 8
   $ inbox     :List of 2
    ..$ info:List of 7
    ..$ view:List of 8
   $ library   :List of 3
    ..$ info    :List of 7
    ..$ query   :List of 8
    ..$ instance:List of 8
   $ m5nr      :List of 10
    ..$ info     :List of 7
    ..$ ontology :List of 8
    ..$ taxonomy :List of 8
    ..$ sources  :List of 8
    ..$ accession:List of 8
    ..$ alias    :List of 8
    ..$ md5      :List of 8
    ..$ function :List of 8
    ..$ organism :List of 8
    ..$ sequence :List of 8
   $ matrix    :List of 4
    ..$ info    :List of 7
    ..$ organism:List of 8
    ..$ function:List of 8
    ..$ feature :List of 8
   $ metadata  :List of 6
    ..$ info    :List of 7
    ..$ template:List of 8
    ..$ cv      :List of 8
    ..$ ontology:List of 8
    ..$ export  :List of 8
    ..$ validate:List of 8
   $ metagenome:List of 3
    ..$ info    :List of 7
    ..$ query   :List of 8
    ..$ instance:List of 8
   $ profile   :List of 2
    ..$ info    :List of 7
    ..$ instance:List of 6
   $ project   :List of 3
    ..$ info    :List of 7
    ..$ query   :List of 8
    ..$ instance:List of 8
   $ sample    :List of 3
    ..$ info    :List of 7
    ..$ query   :List of 8
    ..$ instance:List of 8
   $ server    :List of 2
    ..$ info    :List of 7
    ..$ instance:List of 8
   $ validation:List of 3
    ..$ info    :List of 7
    ..$ template:List of 8
    ..$ data    :List of 8
   $ status    :List of 2
    ..$ info    :List of 7
    ..$ instance:List of 8
  > doc.MGRAST(3)
  List of 15
   $ annotation:List of 3
    ..$ info      :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/annotation"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ sequence  :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/annotation/sequence/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt" "all annotated read sequences from mgm4447943.3 with hits in SwissProt organisms at evaule < e-10"
    .. ..$ name       : chr "sequence"
    .. ..$ description: chr "tab deliminted annotated sequence stream"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "stream"
    .. ..$ attributes :List of 1
    ..$ similarity:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/annotation/similarity/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO" "all annotated read blat stats from mgm4447943.3 with hits in KO functions at % identity > 80"
    .. ..$ name       : chr "similarity"
    .. ..$ description: chr "tab deliminted blast m8 with annotation"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "stream"
    .. ..$ attributes :List of 1
   $ compute   :List of 2
    ..$ info          :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/compute"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ alphadiversity:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/compute/alphadiversity/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/compute/alphadiversity/mgm4447943.3?level=order" "retrieve alpha diversity for order taxon"
    .. ..$ name       : chr "alphadiversity"
    .. ..$ description: chr "Calculate alpha diversity value for given ID and taxon level."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 3
   $ download  :List of 3
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/download"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/download/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/download/mgm4447943.3?file=350.1" "download fasta file of genecalled protein sequences (from stage 350)"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single sequence file."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 1
    ..$ setlist :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/download/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/download/mgm4447943.3?stage=650" "view all available files from stage 650"
    .. ..$ name       : chr "setlist"
    .. ..$ description: chr "Returns a list of sets of sequence files for the given id."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 7
   $ inbox     :List of 2
    ..$ info:List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/inbox"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ view:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/inbox"
    .. ..$ example    : chr [1:2] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/inbox\"" "lists the contents of the user inbox, auth is required"
    .. ..$ name       : chr "view"
    .. ..$ description: chr "lists the contents of the user inbox"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 4
   $ library   :List of 3
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/library"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ query   :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/library"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/library?limit=20&order=name" "retrieve the first 20 libraries ordered by name"
    .. ..$ name       : chr "query"
    .. ..$ description: chr "Returns a set of data matching the query criteria."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 7
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/library/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/library/mgl52924?verbosity=full" "retrieve all data for library mgl52924"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single data object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 10
   $ m5nr      :List of 10
    ..$ info     :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ ontology :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/ontology"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/ontology?source=Subsystems&min_level=level3" "retrieve subsystems hierarchy for the top 3 levels"
    .. ..$ name       : chr "ontology"
    .. ..$ description: chr "Return functional hierarchy"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 3
    ..$ taxonomy :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/taxonomy"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus" "retrieve all class level taxa that belong to Bacteroidetes"
    .. ..$ name       : chr "taxonomy"
    .. ..$ description: chr "Return organism hierarchy"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 3
    ..$ sources  :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/sources"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/sources" "retrieve all data sources for M5NR"
    .. ..$ name       : chr "sources"
    .. ..$ description: chr "Return all sources in M5NR"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 3
    ..$ accession:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/accession/{id}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/accession/YP_003268079.1" "retrieve M5NR data for accession ID 'YP_003268079.1'"
    .. ..$ name       : chr "accession"
    .. ..$ description: chr "Return annotation of given source protein ID"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 8
    ..$ alias    :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/alias/{text}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/alias/IPR001478" "retrieve M5NR data for db_xref ID 'IPR001478'"
    .. ..$ name       : chr "alias"
    .. ..$ description: chr "Return annotations for alias IDs containing the given text"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 8
    ..$ md5      :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/md5/{id}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro" "retrieve InterPro M5NR data for md5sum '000821a2e2f63df1a3873e4b280002a8'"
    .. ..$ name       : chr "md5"
    .. ..$ description: chr "Return annotation(s) or sequence of given md5sum (M5NR ID)"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 8
    ..$ function :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/function/{text}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/function/sulfatase?source=GenBank" "retrieve GenBank M5NR data for function names containing string 'sulfatase'"
    .. ..$ name       : chr "function"
    .. ..$ description: chr "Return annotations for function names containing the given text"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 8
    ..$ organism :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/organism/{text}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/organism/akkermansia?source=KEGG" "retrieve KEGG M5NR data for organism names containing string 'akkermansia'"
    .. ..$ name       : chr "organism"
    .. ..$ description: chr "Return annotations for organism names containing the given text"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 8
    ..$ sequence :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/m5nr/sequence/{text}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL" "retrieve TrEMBL M5NR data for md5sum of sequence 'MAGENHQWQGSIL'"
    .. ..$ name       : chr "sequence"
    .. ..$ description: chr "Return annotation(s) for md5sum (M5NR ID) of given sequence"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 8
   $ matrix    :List of 4
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/matrix"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ organism:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/organism"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
    .. ..$ name       : chr "organism"
    .. ..$ description: chr "Returns a BIOM object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous or asynchronous"
    .. ..$ attributes :List of 14
    ..$ function:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/function"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtere"| __truncated__
    .. ..$ name       : chr "function"
    .. ..$ description: chr "Returns a BIOM object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous or asynchronous"
    .. ..$ attributes :List of 14
    ..$ feature :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/feature"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&"| __truncated__ "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
    .. ..$ name       : chr "feature"
    .. ..$ description: chr "Returns a BIOM object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous or asynchronous"
    .. ..$ attributes :List of 14
   $ metadata  :List of 6
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metadata"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ template:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metadata/template"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metadata/template" "metadata template"
    .. ..$ name       : chr "template"
    .. ..$ description: chr "Returns static template for metadata object relationships and types"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 4
    ..$ cv      :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metadata/cv"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metadata/cv?label=country" "metadata controlled vocabularies"
    .. ..$ name       : chr "cv"
    .. ..$ description: chr "Returns static controlled vocabularies used in metadata. By default returns all CVs at latest version. If label"| __truncated__
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 3
    ..$ ontology:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metadata/ontology"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metadata/ontology?name=biome&version=2013-04-27" "metadata ontology lookup"
    .. ..$ name       : chr "ontology"
    .. ..$ description: chr "Returns static ontology used in metadata for the given name and version."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 6
    ..$ export  :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metadata/export/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metadata/export/mgp128" "all metadata for project mgp128"
    .. ..$ name       : chr "export"
    .. ..$ description: chr "Returns full nested metadata for a project in same format as template, or metadata for a single metagenome."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 5
    ..$ validate:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metadata/validate"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metadata/validate?category=sample&label=material&value=soil" "check if 'soil' is a vaild term for sample material"
    .. ..$ name       : chr "validate"
    .. ..$ description: chr "Validate given metadata value"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 2
   $ metagenome:List of 3
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metagenome"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ query   :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metagenome"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metagenome?limit=20&order=name" "retrieve the first 20 metagenomes ordered by name"
    .. ..$ name       : chr "query"
    .. ..$ description: chr "Returns a set of data matching the query criteria."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 9
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/metagenome/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/metagenome/mgm4447943.3?verbosity=metadata" "retrieve all metadata for metagenome mgm4447943.3"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single data object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 13
   $ profile   :List of 2
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/profile"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ instance:List of 6
    .. ..$ parameters :List of 3
    .. ..$ name       : chr "instance"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes :List of 12
    .. ..$ description: chr "Returns a single data object in BIOM format"
   $ project   :List of 3
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/project"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ query   :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/project"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/project?limit=20&order=name" "retrieve the first 20 projects ordered by name"
    .. ..$ name       : chr "query"
    .. ..$ description: chr "Returns a set of data matching the query criteria."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 7
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/project/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/project/mgp128?verbosity=full" "retrieve all data for project mgp128"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single data object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 13
   $ sample    :List of 3
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/sample"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ query   :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/sample"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/sample?limit=20&order=name" "retrieve the first 20 samples ordered by name"
    .. ..$ name       : chr "query"
    .. ..$ description: chr "Returns a set of data matching the query criteria."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 7
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/sample/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/sample/mgs25823?verbosity=full" "retrieve all data for sample mgs25823"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single data object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 10
   $ server    :List of 2
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/server"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns the server information."
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/server/{ID}"
    .. ..$ example    : chr [1:2] "curl -X GET \"http://api.metagenomics.anl.gov/server/MG-RAST\"" "info for the MG-RAST server"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single user object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 9
   $ validation:List of 3
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/validation"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ template:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/validation/template/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/validation/template/" "validate the communities metagenomics template"
    .. ..$ name       : chr "template"
    .. ..$ description: chr "Checks if the referenced JSON structure is a valid template"
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 2
    ..$ data    :List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/validation/data/{ID}"
    .. ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/validation/data/?template=" "validate a JSON data structure against the MG-RAST metagenome metadata template"
    .. ..$ name       : chr "data"
    .. ..$ description: chr "Returns a single data object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 2
   $ status    :List of 2
    ..$ info    :List of 7
    .. ..$ parameters :List of 3
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/status"
    .. ..$ name       : chr "info"
    .. ..$ type       : chr "synchronous"
    .. ..$ method     : chr "GET"
    .. ..$ attributes : chr "self"
    .. ..$ description: chr "Returns description of parameters and attributes."
    ..$ instance:List of 8
    .. ..$ request    : chr "http://api.metagenomics.anl.gov/status/{TOKEN}"
    .. ..$ example    : chr [1:2] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/status/12345\"" "data for asynchronous call with ID 12345"
    .. ..$ name       : chr "instance"
    .. ..$ description: chr "Returns a single data object."
    .. ..$ parameters :List of 3
    .. ..$ method     : chr "GET"
    .. ..$ type       : chr "synchronous"
    .. ..$ attributes :List of 4
  > 
  > doc.MGRAST (head="matrix")
  List of 4
   $ info    :List of 7
   $ organism:List of 8
   $ function:List of 8
   $ feature :List of 8
  > doc.MGRAST (2, head="matrix")
  List of 4
   $ info    :List of 7
    ..$ parameters :List of 3
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix"
    ..$ name       : chr "info"
    ..$ type       : chr "synchronous"
    ..$ method     : chr "GET"
    ..$ attributes : chr "self"
    ..$ description: chr "Returns description of parameters and attributes."
   $ organism:List of 8
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/organism"
    ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
    ..$ name       : chr "organism"
    ..$ description: chr "Returns a BIOM object."
    ..$ parameters :List of 3
    ..$ method     : chr "GET"
    ..$ type       : chr "synchronous or asynchronous"
    ..$ attributes :List of 14
   $ function:List of 8
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/function"
    ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtere"| __truncated__
    ..$ name       : chr "function"
    ..$ description: chr "Returns a BIOM object."
    ..$ parameters :List of 3
    ..$ method     : chr "GET"
    ..$ type       : chr "synchronous or asynchronous"
    ..$ attributes :List of 14
   $ feature :List of 8
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/feature"
    ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&"| __truncated__ "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
    ..$ name       : chr "feature"
    ..$ description: chr "Returns a BIOM object."
    ..$ parameters :List of 3
    ..$ method     : chr "GET"
    ..$ type       : chr "synchronous or asynchronous"
    ..$ attributes :List of 14
  > doc.MGRAST (3, head="matrix")
  List of 4
   $ info    :List of 7
    ..$ parameters :List of 3
    .. ..$ body    : Named list()
    .. ..$ required: Named list()
    .. ..$ options : Named list()
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix"
    ..$ name       : chr "info"
    ..$ type       : chr "synchronous"
    ..$ method     : chr "GET"
    ..$ attributes : chr "self"
    ..$ description: chr "Returns description of parameters and attributes."
   $ organism:List of 8
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/organism"
    ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
    ..$ name       : chr "organism"
    ..$ description: chr "Returns a BIOM object."
    ..$ parameters :List of 3
    .. ..$ body    : Named list()
    .. ..$ required: Named list()
    .. ..$ options :List of 15
    ..$ method     : chr "GET"
    ..$ type       : chr "synchronous or asynchronous"
    ..$ attributes :List of 14
    .. ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    .. ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    .. ..$ date                : chr [1:2] "date" "time the output data was generated"
    .. ..$ data                :List of 2
    .. ..$ rows                :List of 2
    .. ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    .. ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    .. ..$ format_url          : chr [1:2] "string" "url to the format specification"
    .. ..$ format              : chr [1:2] "string" "format specification name"
    .. ..$ columns             :List of 2
    .. ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    .. ..$ shape               :List of 2
    .. ..$ id                  : chr [1:2] "string" "unique object identifier"
    .. ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ function:List of 8
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/function"
    ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtere"| __truncated__
    ..$ name       : chr "function"
    ..$ description: chr "Returns a BIOM object."
    ..$ parameters :List of 3
    .. ..$ body    : Named list()
    .. ..$ required: Named list()
    .. ..$ options :List of 13
    ..$ method     : chr "GET"
    ..$ type       : chr "synchronous or asynchronous"
    ..$ attributes :List of 14
    .. ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    .. ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    .. ..$ date                : chr [1:2] "date" "time the output data was generated"
    .. ..$ data                :List of 2
    .. ..$ rows                :List of 2
    .. ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    .. ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    .. ..$ format_url          : chr [1:2] "string" "url to the format specification"
    .. ..$ format              : chr [1:2] "string" "format specification name"
    .. ..$ columns             :List of 2
    .. ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    .. ..$ shape               :List of 2
    .. ..$ id                  : chr [1:2] "string" "unique object identifier"
    .. ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ feature :List of 8
    ..$ request    : chr "http://api.metagenomics.anl.gov/matrix/feature"
    ..$ example    : chr [1:2] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&"| __truncated__ "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
    ..$ name       : chr "feature"
    ..$ description: chr "Returns a BIOM object."
    ..$ parameters :List of 3
    .. ..$ body    : Named list()
    .. ..$ required: Named list()
    .. ..$ options :List of 11
    ..$ method     : chr "GET"
    ..$ type       : chr "synchronous or asynchronous"
    ..$ attributes :List of 14
    .. ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    .. ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    .. ..$ date                : chr [1:2] "date" "time the output data was generated"
    .. ..$ data                :List of 2
    .. ..$ rows                :List of 2
    .. ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    .. ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    .. ..$ format_url          : chr [1:2] "string" "url to the format specification"
    .. ..$ format              : chr [1:2] "string" "format specification name"
    .. ..$ columns             :List of 2
    .. ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    .. ..$ shape               :List of 2
    .. ..$ id                  : chr [1:2] "string" "unique object identifier"
    .. ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
  > 
  > doc.MGRAST (stratum="parameters")
  List of 51
   $ annotation.info.parameters       :List of 3
   $ annotation.sequence.parameters   :List of 3
   $ annotation.similarity.parameters :List of 3
   $ compute.info.parameters          :List of 3
   $ compute.alphadiversity.parameters:List of 3
   $ download.info.parameters         :List of 3
   $ download.instance.parameters     :List of 3
   $ download.setlist.parameters      :List of 3
   $ inbox.info.parameters            :List of 3
   $ inbox.view.parameters            :List of 3
   $ library.info.parameters          :List of 3
   $ library.query.parameters         :List of 3
   $ library.instance.parameters      :List of 3
   $ m5nr.info.parameters             :List of 3
   $ m5nr.ontology.parameters         :List of 3
   $ m5nr.taxonomy.parameters         :List of 3
   $ m5nr.sources.parameters          :List of 3
   $ m5nr.accession.parameters        :List of 3
   $ m5nr.alias.parameters            :List of 3
   $ m5nr.md5.parameters              :List of 3
   $ m5nr.function.parameters         :List of 3
   $ m5nr.organism.parameters         :List of 3
   $ m5nr.sequence.parameters         :List of 3
   $ matrix.info.parameters           :List of 3
   $ matrix.organism.parameters       :List of 3
   $ matrix.function.parameters       :List of 3
   $ matrix.feature.parameters        :List of 3
   $ metadata.info.parameters         :List of 3
   $ metadata.template.parameters     :List of 3
   $ metadata.cv.parameters           :List of 3
   $ metadata.ontology.parameters     :List of 3
   $ metadata.export.parameters       :List of 3
   $ metadata.validate.parameters     :List of 3
   $ metagenome.info.parameters       :List of 3
   $ metagenome.query.parameters      :List of 3
   $ metagenome.instance.parameters   :List of 3
   $ profile.info.parameters          :List of 3
   $ profile.instance.parameters      :List of 3
   $ project.info.parameters          :List of 3
   $ project.query.parameters         :List of 3
   $ project.instance.parameters      :List of 3
   $ sample.info.parameters           :List of 3
   $ sample.query.parameters          :List of 3
   $ sample.instance.parameters       :List of 3
   $ server.info.parameters           :List of 3
   $ server.instance.parameters       :List of 3
   $ validation.info.parameters       :List of 3
   $ validation.template.parameters   :List of 3
   $ validation.data.parameters       :List of 3
   $ status.info.parameters           :List of 3
   $ status.instance.parameters       :List of 3
  > doc.MGRAST (2, stratum="parameters")
  List of 51
   $ annotation.info.parameters       :List of 3
    ..$ body    : Named list()
    ..$ options : Named list()
    ..$ required: Named list()
   $ annotation.sequence.parameters   :List of 3
    ..$ body    : Named list()
    ..$ options :List of 7
    ..$ required:List of 1
   $ annotation.similarity.parameters :List of 3
    ..$ body    : Named list()
    ..$ options :List of 7
    ..$ required:List of 1
   $ compute.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ compute.alphadiversity.parameters:List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 2
   $ download.info.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ download.instance.parameters     :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ download.setlist.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ inbox.info.parameters            :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ inbox.view.parameters            :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options : Named list()
   $ library.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ library.query.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 4
   $ library.instance.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ m5nr.info.parameters             :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ m5nr.ontology.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 6
   $ m5nr.taxonomy.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 5
   $ m5nr.sources.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 1
   $ m5nr.accession.parameters        :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 4
   $ m5nr.alias.parameters            :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 6
   $ m5nr.md5.parameters              :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 7
   $ m5nr.function.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 7
   $ m5nr.organism.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 8
   $ m5nr.sequence.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 5
   $ matrix.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ matrix.organism.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 15
   $ matrix.function.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 13
   $ matrix.feature.parameters        :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 11
   $ metadata.info.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ metadata.template.parameters     :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ metadata.cv.parameters           :List of 3
    ..$ body    : Named list()
    ..$ options :List of 2
    ..$ required: Named list()
   $ metadata.ontology.parameters     :List of 3
    ..$ body    : Named list()
    ..$ options : Named list()
    ..$ required:List of 2
   $ metadata.export.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options : Named list()
   $ metadata.validate.parameters     :List of 3
    ..$ body    : Named list()
    ..$ options :List of 5
    ..$ required: Named list()
   $ metagenome.info.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ metagenome.query.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 11
   $ metagenome.instance.parameters   :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ profile.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ profile.instance.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 6
   $ project.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ project.query.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 4
   $ project.instance.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ sample.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ sample.query.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 3
   $ sample.instance.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ server.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ server.instance.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options : Named list()
   $ validation.info.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ validation.template.parameters   :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options : Named list()
   $ validation.data.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
   $ status.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ status.instance.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    ..$ options :List of 1
  > doc.MGRAST (3, stratum="parameters")
  List of 51
   $ annotation.info.parameters       :List of 3
    ..$ body    : Named list()
    ..$ options : Named list()
    ..$ required: Named list()
   $ annotation.sequence.parameters   :List of 3
    ..$ body    : Named list()
    ..$ options :List of 7
    .. ..$ source      :List of 2
    .. ..$ length      : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    .. ..$ identity    : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    .. ..$ evalue      : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    .. ..$ filter      : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
    .. ..$ type        :List of 2
    .. ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ annotation.similarity.parameters :List of 3
    ..$ body    : Named list()
    ..$ options :List of 7
    .. ..$ source      :List of 2
    .. ..$ length      : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    .. ..$ identity    : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    .. ..$ evalue      : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    .. ..$ filter      : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
    .. ..$ type        :List of 2
    .. ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ compute.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ compute.alphadiversity.parameters:List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options :List of 2
    .. ..$ source:List of 2
    .. ..$ level :List of 2
   $ download.info.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ download.instance.parameters     :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
    ..$ options :List of 1
    .. ..$ file: chr [1:2] "string" "file name or identifier"
   $ download.setlist.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
    ..$ options :List of 1
    .. ..$ stage: chr [1:2] "string" "stage name or identifier"
   $ inbox.info.parameters            :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ inbox.view.parameters            :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ auth: chr [1:2] "string" "unique string of text generated by MG-RAST for your account"
    ..$ options : Named list()
   $ library.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ library.query.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 4
    .. ..$ verbosity:List of 2
    .. ..$ order    :List of 2
    .. ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ library.instance.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options :List of 1
    .. ..$ verbosity:List of 2
   $ m5nr.info.parameters             :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ m5nr.ontology.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 6
    .. ..$ source      :List of 2
    .. ..$ version     : chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ filter      : chr [1:2] "string" "text of ontology group (filter_level) to filter by"
    .. ..$ exact       : chr [1:2] "boolean" "if true return only those ontologies that exactly match filter, default is false"
    .. ..$ filter_level:List of 2
    .. ..$ min_level   :List of 2
   $ m5nr.taxonomy.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 5
    .. ..$ version     : chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ filter      : chr [1:2] "string" "text of taxanomy group (filter_level) to filter by"
    .. ..$ exact       : chr [1:2] "boolean" "if true return only those taxonomies that exactly match filter, default is false"
    .. ..$ filter_level:List of 2
    .. ..$ min_level   :List of 2
   $ m5nr.sources.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 1
    .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
   $ m5nr.accession.parameters        :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique identifier from source DB"
    ..$ options :List of 4
    .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    .. ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.alias.parameters            :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ text: chr [1:2] "string" "text string of partial alias"
    ..$ options :List of 6
    .. ..$ source : chr [1:2] "string" "source name to restrict search by"
    .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    .. ..$ exact  : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    .. ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.md5.parameters              :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique identifier in form of md5 checksum"
    ..$ options :List of 7
    .. ..$ source  : chr [1:2] "string" "source name to restrict search by"
    .. ..$ format  :List of 2
    .. ..$ sequence: chr [1:2] "boolean" "if true return sequence output, else return annotation output, default is false"
    .. ..$ version : chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ order   : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    .. ..$ limit   : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset  : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.function.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ text: chr [1:2] "string" "text string of partial function name"
    ..$ options :List of 7
    .. ..$ source : chr [1:2] "string" "source name to restrict search by"
    .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    .. ..$ exact  : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    .. ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
    .. ..$ inverse: chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
   $ m5nr.organism.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ text: chr [1:2] "string" "text string of partial organism name"
    ..$ options :List of 8
    .. ..$ source   : chr [1:2] "string" "source name to restrict search by"
    .. ..$ version  : chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ exact    : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    .. ..$ inverse  : chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
    .. ..$ order    : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    .. ..$ tax_level:List of 2
    .. ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.sequence.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ text: chr [1:2] "string" "text string of protein sequence"
    ..$ options :List of 5
    .. ..$ source : chr [1:2] "string" "source name to restrict search by"
    .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    .. ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    .. ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ matrix.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ matrix.organism.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 15
    .. ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    .. ..$ source       :List of 2
    .. ..$ result_type  :List of 2
    .. ..$ filter       : chr [1:2] "string" "filter the return results to only include abundances based on genes with this function"
    .. ..$ group_level  :List of 2
    .. ..$ taxid        : chr [1:2] "boolean" "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
    .. ..$ grep         : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
    .. ..$ length       : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    .. ..$ evalue       : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    .. ..$ identity     : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    .. ..$ filter_source:List of 2
    .. ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    .. ..$ id           : chr [1:2] "string" "one or more metagenome or project unique identifier"
    .. ..$ filter_level :List of 2
    .. ..$ hit_type     :List of 2
   $ matrix.function.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 13
    .. ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    .. ..$ source       :List of 2
    .. ..$ result_type  :List of 2
    .. ..$ filter       : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
    .. ..$ group_level  :List of 2
    .. ..$ grep         : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
    .. ..$ length       : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    .. ..$ evalue       : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    .. ..$ identity     : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    .. ..$ filter_source:List of 2
    .. ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    .. ..$ id           : chr [1:2] "string" "one or more metagenome or project unique identifier"
    .. ..$ filter_level :List of 2
   $ matrix.feature.parameters        :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 11
    .. ..$ asynchronous   : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    .. ..$ source         :List of 2
    .. ..$ result_type    :List of 2
    .. ..$ filter         : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
    .. ..$ length         : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    .. ..$ evalue         : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    .. ..$ identity       : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    .. ..$ hide_annotation: chr [1:2] "boolean" "if true do not return feature metadata in 'rows' object, default is false"
    .. ..$ id             : chr [1:2] "string" "one or more metagenome or project unique identifier"
    .. ..$ hide_metadata  : chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    .. ..$ filter_level   :List of 2
   $ metadata.info.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ metadata.template.parameters     :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ metadata.cv.parameters           :List of 3
    ..$ body    : Named list()
    ..$ options :List of 2
    .. ..$ version: chr [1:2] "string" "version of CV select list or ontology to use"
    .. ..$ label  : chr [1:2] "string" "metadata label"
    ..$ required: Named list()
   $ metadata.ontology.parameters     :List of 3
    ..$ body    : Named list()
    ..$ options : Named list()
    ..$ required:List of 2
    .. ..$ version: chr [1:2] "string" "version of ontology to use"
    .. ..$ name   : chr [1:2] "string" "ontology name"
   $ metadata.export.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options : Named list()
   $ metadata.validate.parameters     :List of 3
    ..$ body    : Named list()
    ..$ options :List of 5
    .. ..$ group   :List of 2
    .. ..$ version : chr [1:2] "string" "version of CV select list or ontology to use"
    .. ..$ value   : chr [1:2] "string" "metadata value"
    .. ..$ label   : chr [1:2] "string" "metadata label"
    .. ..$ category:List of 2
    ..$ required: Named list()
   $ metagenome.info.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ metagenome.query.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 11
    .. ..$ verbosity:List of 2
    .. ..$ function : chr [1:2] "string" "search parameter: query string for function"
    .. ..$ status   :List of 2
    .. ..$ match    :List of 2
    .. ..$ direction:List of 2
    .. ..$ order    : chr [1:2] "string" "metagenome object field to sort by (default is id)"
    .. ..$ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
    .. ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ md5      : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
    .. ..$ organism : chr [1:2] "string" "search parameter: query string for organism"
    .. ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ metagenome.instance.parameters   :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options :List of 1
    .. ..$ verbosity:List of 2
   $ profile.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ profile.instance.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options :List of 6
    .. ..$ source  :List of 2
    .. ..$ length  : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    .. ..$ identity: chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    .. ..$ evalue  : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    .. ..$ type    :List of 2
    .. ..$ hit_type:List of 2
   $ project.info.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ project.query.parameters         :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 4
    .. ..$ verbosity:List of 2
    .. ..$ order    :List of 2
    .. ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ project.instance.parameters      :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options :List of 1
    .. ..$ verbosity:List of 2
   $ sample.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ sample.query.parameters          :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options :List of 3
    .. ..$ order :List of 2
    .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
    .. ..$ offset: chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ sample.instance.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique object identifier"
    ..$ options :List of 1
    .. ..$ verbosity:List of 2
   $ server.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ server.instance.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique server ID"
    ..$ options : Named list()
   $ validation.info.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ validation.template.parameters   :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "SHOCK template id"
    ..$ options : Named list()
   $ validation.data.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "SHOCK data id"
    ..$ options :List of 1
    .. ..$ template: chr [1:2] "string" "SHOCK template id, default is MG-RAST metagenome metadata template"
   $ status.info.parameters           :List of 3
    ..$ body    : Named list()
    ..$ required: Named list()
    ..$ options : Named list()
   $ status.instance.parameters       :List of 3
    ..$ body    : Named list()
    ..$ required:List of 1
    .. ..$ id: chr [1:2] "string" "unique process id"
    ..$ options :List of 1
    .. ..$ verbosity:List of 2
  > 
  > doc.MGRAST (stratum="options")
  List of 51
   $ annotation.info.parameters.options       : Named list()
   $ annotation.sequence.parameters.options   :List of 7
   $ annotation.similarity.parameters.options :List of 7
   $ compute.info.parameters.options          : Named list()
   $ compute.alphadiversity.parameters.options:List of 2
   $ download.info.parameters.options         : Named list()
   $ download.instance.parameters.options     :List of 1
   $ download.setlist.parameters.options      :List of 1
   $ inbox.info.parameters.options            : Named list()
   $ inbox.view.parameters.options            : Named list()
   $ library.info.parameters.options          : Named list()
   $ library.query.parameters.options         :List of 4
   $ library.instance.parameters.options      :List of 1
   $ m5nr.info.parameters.options             : Named list()
   $ m5nr.ontology.parameters.options         :List of 6
   $ m5nr.taxonomy.parameters.options         :List of 5
   $ m5nr.sources.parameters.options          :List of 1
   $ m5nr.accession.parameters.options        :List of 4
   $ m5nr.alias.parameters.options            :List of 6
   $ m5nr.md5.parameters.options              :List of 7
   $ m5nr.function.parameters.options         :List of 7
   $ m5nr.organism.parameters.options         :List of 8
   $ m5nr.sequence.parameters.options         :List of 5
   $ matrix.info.parameters.options           : Named list()
   $ matrix.organism.parameters.options       :List of 15
   $ matrix.function.parameters.options       :List of 13
   $ matrix.feature.parameters.options        :List of 11
   $ metadata.info.parameters.options         : Named list()
   $ metadata.template.parameters.options     : Named list()
   $ metadata.cv.parameters.options           :List of 2
   $ metadata.ontology.parameters.options     : Named list()
   $ metadata.export.parameters.options       : Named list()
   $ metadata.validate.parameters.options     :List of 5
   $ metagenome.info.parameters.options       : Named list()
   $ metagenome.query.parameters.options      :List of 11
   $ metagenome.instance.parameters.options   :List of 1
   $ profile.info.parameters.options          : Named list()
   $ profile.instance.parameters.options      :List of 6
   $ project.info.parameters.options          : Named list()
   $ project.query.parameters.options         :List of 4
   $ project.instance.parameters.options      :List of 1
   $ sample.info.parameters.options           : Named list()
   $ sample.query.parameters.options          :List of 3
   $ sample.instance.parameters.options       :List of 1
   $ server.info.parameters.options           : Named list()
   $ server.instance.parameters.options       : Named list()
   $ validation.info.parameters.options       : Named list()
   $ validation.template.parameters.options   : Named list()
   $ validation.data.parameters.options       :List of 1
   $ status.info.parameters.options           : Named list()
   $ status.instance.parameters.options       :List of 1
  > doc.MGRAST (2, stratum="options")
  List of 51
   $ annotation.info.parameters.options       : Named list()
   $ annotation.sequence.parameters.options   :List of 7
    ..$ source      :List of 2
    ..$ length      : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ identity    : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ evalue      : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ filter      : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
    ..$ type        :List of 2
    ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
   $ annotation.similarity.parameters.options :List of 7
    ..$ source      :List of 2
    ..$ length      : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ identity    : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ evalue      : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ filter      : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
    ..$ type        :List of 2
    ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
   $ compute.info.parameters.options          : Named list()
   $ compute.alphadiversity.parameters.options:List of 2
    ..$ source:List of 2
    ..$ level :List of 2
   $ download.info.parameters.options         : Named list()
   $ download.instance.parameters.options     :List of 1
    ..$ file: chr [1:2] "string" "file name or identifier"
   $ download.setlist.parameters.options      :List of 1
    ..$ stage: chr [1:2] "string" "stage name or identifier"
   $ inbox.info.parameters.options            : Named list()
   $ inbox.view.parameters.options            : Named list()
   $ library.info.parameters.options          : Named list()
   $ library.query.parameters.options         :List of 4
    ..$ verbosity:List of 2
    ..$ order    :List of 2
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ library.instance.parameters.options      :List of 1
    ..$ verbosity:List of 2
   $ m5nr.info.parameters.options             : Named list()
   $ m5nr.ontology.parameters.options         :List of 6
    ..$ source      :List of 2
    ..$ version     : chr [1:2] "integer" "M5NR version, default 10"
    ..$ filter      : chr [1:2] "string" "text of ontology group (filter_level) to filter by"
    ..$ exact       : chr [1:2] "boolean" "if true return only those ontologies that exactly match filter, default is false"
    ..$ filter_level:List of 2
    ..$ min_level   :List of 2
   $ m5nr.taxonomy.parameters.options         :List of 5
    ..$ version     : chr [1:2] "integer" "M5NR version, default 10"
    ..$ filter      : chr [1:2] "string" "text of taxanomy group (filter_level) to filter by"
    ..$ exact       : chr [1:2] "boolean" "if true return only those taxonomies that exactly match filter, default is false"
    ..$ filter_level:List of 2
    ..$ min_level   :List of 2
   $ m5nr.sources.parameters.options          :List of 1
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
   $ m5nr.accession.parameters.options        :List of 4
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.alias.parameters.options            :List of 6
    ..$ source : chr [1:2] "string" "source name to restrict search by"
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ exact  : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.md5.parameters.options              :List of 7
    ..$ source  : chr [1:2] "string" "source name to restrict search by"
    ..$ format  :List of 2
    ..$ sequence: chr [1:2] "boolean" "if true return sequence output, else return annotation output, default is false"
    ..$ version : chr [1:2] "integer" "M5NR version, default 10"
    ..$ order   : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit   : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset  : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.function.parameters.options         :List of 7
    ..$ source : chr [1:2] "string" "source name to restrict search by"
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ exact  : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
    ..$ inverse: chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
   $ m5nr.organism.parameters.options         :List of 8
    ..$ source   : chr [1:2] "string" "source name to restrict search by"
    ..$ version  : chr [1:2] "integer" "M5NR version, default 10"
    ..$ exact    : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    ..$ inverse  : chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
    ..$ order    : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ tax_level:List of 2
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.sequence.parameters.options         :List of 5
    ..$ source : chr [1:2] "string" "source name to restrict search by"
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ matrix.info.parameters.options           : Named list()
   $ matrix.organism.parameters.options       :List of 15
    ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    ..$ source       :List of 2
    ..$ result_type  :List of 2
    ..$ filter       : chr [1:2] "string" "filter the return results to only include abundances based on genes with this function"
    ..$ group_level  :List of 2
    ..$ taxid        : chr [1:2] "boolean" "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
    ..$ grep         : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
    ..$ length       : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ evalue       : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ identity     : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ filter_source:List of 2
    ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    ..$ id           : chr [1:2] "string" "one or more metagenome or project unique identifier"
    ..$ filter_level :List of 2
    ..$ hit_type     :List of 2
   $ matrix.function.parameters.options       :List of 13
    ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    ..$ source       :List of 2
    ..$ result_type  :List of 2
    ..$ filter       : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
    ..$ group_level  :List of 2
    ..$ grep         : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
    ..$ length       : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ evalue       : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ identity     : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ filter_source:List of 2
    ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    ..$ id           : chr [1:2] "string" "one or more metagenome or project unique identifier"
    ..$ filter_level :List of 2
   $ matrix.feature.parameters.options        :List of 11
    ..$ asynchronous   : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    ..$ source         :List of 2
    ..$ result_type    :List of 2
    ..$ filter         : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
    ..$ length         : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ evalue         : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ identity       : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ hide_annotation: chr [1:2] "boolean" "if true do not return feature metadata in 'rows' object, default is false"
    ..$ id             : chr [1:2] "string" "one or more metagenome or project unique identifier"
    ..$ hide_metadata  : chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    ..$ filter_level   :List of 2
   $ metadata.info.parameters.options         : Named list()
   $ metadata.template.parameters.options     : Named list()
   $ metadata.cv.parameters.options           :List of 2
    ..$ version: chr [1:2] "string" "version of CV select list or ontology to use"
    ..$ label  : chr [1:2] "string" "metadata label"
   $ metadata.ontology.parameters.options     : Named list()
   $ metadata.export.parameters.options       : Named list()
   $ metadata.validate.parameters.options     :List of 5
    ..$ group   :List of 2
    ..$ version : chr [1:2] "string" "version of CV select list or ontology to use"
    ..$ value   : chr [1:2] "string" "metadata value"
    ..$ label   : chr [1:2] "string" "metadata label"
    ..$ category:List of 2
   $ metagenome.info.parameters.options       : Named list()
   $ metagenome.query.parameters.options      :List of 11
    ..$ verbosity:List of 2
    ..$ function : chr [1:2] "string" "search parameter: query string for function"
    ..$ status   :List of 2
    ..$ match    :List of 2
    ..$ direction:List of 2
    ..$ order    : chr [1:2] "string" "metagenome object field to sort by (default is id)"
    ..$ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ md5      : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
    ..$ organism : chr [1:2] "string" "search parameter: query string for organism"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ metagenome.instance.parameters.options   :List of 1
    ..$ verbosity:List of 2
   $ profile.info.parameters.options          : Named list()
   $ profile.instance.parameters.options      :List of 6
    ..$ source  :List of 2
    ..$ length  : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ identity: chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ evalue  : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ type    :List of 2
    ..$ hit_type:List of 2
   $ project.info.parameters.options          : Named list()
   $ project.query.parameters.options         :List of 4
    ..$ verbosity:List of 2
    ..$ order    :List of 2
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ project.instance.parameters.options      :List of 1
    ..$ verbosity:List of 2
   $ sample.info.parameters.options           : Named list()
   $ sample.query.parameters.options          :List of 3
    ..$ order :List of 2
    ..$ limit : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset: chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ sample.instance.parameters.options       :List of 1
    ..$ verbosity:List of 2
   $ server.info.parameters.options           : Named list()
   $ server.instance.parameters.options       : Named list()
   $ validation.info.parameters.options       : Named list()
   $ validation.template.parameters.options   : Named list()
   $ validation.data.parameters.options       :List of 1
    ..$ template: chr [1:2] "string" "SHOCK template id, default is MG-RAST metagenome metadata template"
   $ status.info.parameters.options           : Named list()
   $ status.instance.parameters.options       :List of 1
    ..$ verbosity:List of 2
  > doc.MGRAST (3, stratum="options")
  List of 51
   $ annotation.info.parameters.options       : Named list()
   $ annotation.sequence.parameters.options   :List of 7
    ..$ source      :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 16
    ..$ length      : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ identity    : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ evalue      : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ filter      : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
    ..$ type        :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 5
    ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
   $ annotation.similarity.parameters.options :List of 7
    ..$ source      :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 16
    ..$ length      : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ identity    : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ evalue      : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ filter      : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
    ..$ type        :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 5
    ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
   $ compute.info.parameters.options          : Named list()
   $ compute.alphadiversity.parameters.options:List of 2
    ..$ source:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 12
    ..$ level :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 8
   $ download.info.parameters.options         : Named list()
   $ download.instance.parameters.options     :List of 1
    ..$ file: chr [1:2] "string" "file name or identifier"
   $ download.setlist.parameters.options      :List of 1
    ..$ stage: chr [1:2] "string" "stage name or identifier"
   $ inbox.info.parameters.options            : Named list()
   $ inbox.view.parameters.options            : Named list()
   $ library.info.parameters.options          : Named list()
   $ library.query.parameters.options         :List of 4
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 1
    ..$ order    :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ library.instance.parameters.options      :List of 1
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
   $ m5nr.info.parameters.options             : Named list()
   $ m5nr.ontology.parameters.options         :List of 6
    ..$ source      :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ version     : chr [1:2] "integer" "M5NR version, default 10"
    ..$ filter      : chr [1:2] "string" "text of ontology group (filter_level) to filter by"
    ..$ exact       : chr [1:2] "boolean" "if true return only those ontologies that exactly match filter, default is false"
    ..$ filter_level:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ min_level   :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
   $ m5nr.taxonomy.parameters.options         :List of 5
    ..$ version     : chr [1:2] "integer" "M5NR version, default 10"
    ..$ filter      : chr [1:2] "string" "text of taxanomy group (filter_level) to filter by"
    ..$ exact       : chr [1:2] "boolean" "if true return only those taxonomies that exactly match filter, default is false"
    ..$ filter_level:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 7
    ..$ min_level   :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 7
   $ m5nr.sources.parameters.options          :List of 1
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
   $ m5nr.accession.parameters.options        :List of 4
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.alias.parameters.options            :List of 6
    ..$ source : chr [1:2] "string" "source name to restrict search by"
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ exact  : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.md5.parameters.options              :List of 7
    ..$ source  : chr [1:2] "string" "source name to restrict search by"
    ..$ format  :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ sequence: chr [1:2] "boolean" "if true return sequence output, else return annotation output, default is false"
    ..$ version : chr [1:2] "integer" "M5NR version, default 10"
    ..$ order   : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit   : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset  : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.function.parameters.options         :List of 7
    ..$ source : chr [1:2] "string" "source name to restrict search by"
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ exact  : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
    ..$ inverse: chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
   $ m5nr.organism.parameters.options         :List of 8
    ..$ source   : chr [1:2] "string" "source name to restrict search by"
    ..$ version  : chr [1:2] "integer" "M5NR version, default 10"
    ..$ exact    : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
    ..$ inverse  : chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
    ..$ order    : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ tax_level:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 8
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ m5nr.sequence.parameters.options         :List of 5
    ..$ source : chr [1:2] "string" "source name to restrict search by"
    ..$ version: chr [1:2] "integer" "M5NR version, default 10"
    ..$ order  : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit  : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ matrix.info.parameters.options           : Named list()
   $ matrix.organism.parameters.options       :List of 15
    ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    ..$ source       :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 14
    ..$ result_type  :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ filter       : chr [1:2] "string" "filter the return results to only include abundances based on genes with this function"
    ..$ group_level  :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 8
    ..$ taxid        : chr [1:2] "boolean" "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
    ..$ grep         : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
    ..$ length       : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ evalue       : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ identity     : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ filter_source:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    ..$ id           : chr [1:2] "string" "one or more metagenome or project unique identifier"
    ..$ filter_level :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ hit_type     :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
   $ matrix.function.parameters.options       :List of 13
    ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    ..$ source       :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ result_type  :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ filter       : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
    ..$ group_level  :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ grep         : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
    ..$ length       : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ evalue       : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ identity     : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ filter_source:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 14
    ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    ..$ id           : chr [1:2] "string" "one or more metagenome or project unique identifier"
    ..$ filter_level :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 8
   $ matrix.feature.parameters.options        :List of 11
    ..$ asynchronous   : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
    ..$ source         :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 12
    ..$ result_type    :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
    ..$ filter         : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
    ..$ length         : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ evalue         : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ identity       : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ hide_annotation: chr [1:2] "boolean" "if true do not return feature metadata in 'rows' object, default is false"
    ..$ id             : chr [1:2] "string" "one or more metagenome or project unique identifier"
    ..$ hide_metadata  : chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
    ..$ filter_level   :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 8
   $ metadata.info.parameters.options         : Named list()
   $ metadata.template.parameters.options     : Named list()
   $ metadata.cv.parameters.options           :List of 2
    ..$ version: chr [1:2] "string" "version of CV select list or ontology to use"
    ..$ label  : chr [1:2] "string" "metadata label"
   $ metadata.ontology.parameters.options     : Named list()
   $ metadata.export.parameters.options       : Named list()
   $ metadata.validate.parameters.options     :List of 5
    ..$ group   :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
    ..$ version : chr [1:2] "string" "version of CV select list or ontology to use"
    ..$ value   : chr [1:2] "string" "metadata value"
    ..$ label   : chr [1:2] "string" "metadata label"
    ..$ category:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
   $ metagenome.info.parameters.options       : Named list()
   $ metagenome.query.parameters.options      :List of 11
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 5
    ..$ function : chr [1:2] "string" "search parameter: query string for function"
    ..$ status   :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
    ..$ match    :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ direction:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ order    : chr [1:2] "string" "metagenome object field to sort by (default is id)"
    ..$ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ md5      : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
    ..$ organism : chr [1:2] "string" "search parameter: query string for organism"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ metagenome.instance.parameters.options   :List of 1
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 4
   $ profile.info.parameters.options          : Named list()
   $ profile.instance.parameters.options      :List of 6
    ..$ source  :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 18
    ..$ length  : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
    ..$ identity: chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
    ..$ evalue  : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
    ..$ type    :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
    ..$ hit_type:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
   $ project.info.parameters.options          : Named list()
   $ project.query.parameters.options         :List of 4
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
    ..$ order    :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ limit    : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ project.instance.parameters.options      :List of 1
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
   $ sample.info.parameters.options           : Named list()
   $ sample.query.parameters.options          :List of 3
    ..$ order :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ limit : chr [1:2] "integer" "maximum number of items requested"
    ..$ offset: chr [1:2] "integer" "zero based index of the first data object to be returned"
   $ sample.instance.parameters.options       :List of 1
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 3
   $ server.info.parameters.options           : Named list()
   $ server.instance.parameters.options       : Named list()
   $ validation.info.parameters.options       : Named list()
   $ validation.template.parameters.options   : Named list()
   $ validation.data.parameters.options       :List of 1
    ..$ template: chr [1:2] "string" "SHOCK template id, default is MG-RAST metagenome metadata template"
   $ status.info.parameters.options           : Named list()
   $ status.instance.parameters.options       :List of 1
    ..$ verbosity:List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
  > 
  > doc.MGRAST (stratum="required")
  List of 51
   $ annotation.info.parameters.required       : Named list()
   $ annotation.sequence.parameters.required   :List of 1
   $ annotation.similarity.parameters.required :List of 1
   $ compute.info.parameters.required          : Named list()
   $ compute.alphadiversity.parameters.required:List of 1
   $ download.info.parameters.required         : Named list()
   $ download.instance.parameters.required     :List of 1
   $ download.setlist.parameters.required      :List of 1
   $ inbox.info.parameters.required            : Named list()
   $ inbox.view.parameters.required            :List of 1
   $ library.info.parameters.required          : Named list()
   $ library.query.parameters.required         : Named list()
   $ library.instance.parameters.required      :List of 1
   $ m5nr.info.parameters.required             : Named list()
   $ m5nr.ontology.parameters.required         : Named list()
   $ m5nr.taxonomy.parameters.required         : Named list()
   $ m5nr.sources.parameters.required          : Named list()
   $ m5nr.accession.parameters.required        :List of 1
   $ m5nr.alias.parameters.required            :List of 1
   $ m5nr.md5.parameters.required              :List of 1
   $ m5nr.function.parameters.required         :List of 1
   $ m5nr.organism.parameters.required         :List of 1
   $ m5nr.sequence.parameters.required         :List of 1
   $ matrix.info.parameters.required           : Named list()
   $ matrix.organism.parameters.required       : Named list()
   $ matrix.function.parameters.required       : Named list()
   $ matrix.feature.parameters.required        : Named list()
   $ metadata.info.parameters.required         : Named list()
   $ metadata.template.parameters.required     : Named list()
   $ metadata.cv.parameters.required           : Named list()
   $ metadata.ontology.parameters.required     :List of 2
   $ metadata.export.parameters.required       :List of 1
   $ metadata.validate.parameters.required     : Named list()
   $ metagenome.info.parameters.required       : Named list()
   $ metagenome.query.parameters.required      : Named list()
   $ metagenome.instance.parameters.required   :List of 1
   $ profile.info.parameters.required          : Named list()
   $ profile.instance.parameters.required      :List of 1
   $ project.info.parameters.required          : Named list()
   $ project.query.parameters.required         : Named list()
   $ project.instance.parameters.required      :List of 1
   $ sample.info.parameters.required           : Named list()
   $ sample.query.parameters.required          : Named list()
   $ sample.instance.parameters.required       :List of 1
   $ server.info.parameters.required           : Named list()
   $ server.instance.parameters.required       :List of 1
   $ validation.info.parameters.required       : Named list()
   $ validation.template.parameters.required   :List of 1
   $ validation.data.parameters.required       :List of 1
   $ status.info.parameters.required           : Named list()
   $ status.instance.parameters.required       :List of 1
  > doc.MGRAST (2, stratum="required")
  List of 51
   $ annotation.info.parameters.required       : Named list()
   $ annotation.sequence.parameters.required   :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ annotation.similarity.parameters.required :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ compute.info.parameters.required          : Named list()
   $ compute.alphadiversity.parameters.required:List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ download.info.parameters.required         : Named list()
   $ download.instance.parameters.required     :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ download.setlist.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ inbox.info.parameters.required            : Named list()
   $ inbox.view.parameters.required            :List of 1
    ..$ auth: chr [1:2] "string" "unique string of text generated by MG-RAST for your account"
   $ library.info.parameters.required          : Named list()
   $ library.query.parameters.required         : Named list()
   $ library.instance.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ m5nr.info.parameters.required             : Named list()
   $ m5nr.ontology.parameters.required         : Named list()
   $ m5nr.taxonomy.parameters.required         : Named list()
   $ m5nr.sources.parameters.required          : Named list()
   $ m5nr.accession.parameters.required        :List of 1
    ..$ id: chr [1:2] "string" "unique identifier from source DB"
   $ m5nr.alias.parameters.required            :List of 1
    ..$ text: chr [1:2] "string" "text string of partial alias"
   $ m5nr.md5.parameters.required              :List of 1
    ..$ id: chr [1:2] "string" "unique identifier in form of md5 checksum"
   $ m5nr.function.parameters.required         :List of 1
    ..$ text: chr [1:2] "string" "text string of partial function name"
   $ m5nr.organism.parameters.required         :List of 1
    ..$ text: chr [1:2] "string" "text string of partial organism name"
   $ m5nr.sequence.parameters.required         :List of 1
    ..$ text: chr [1:2] "string" "text string of protein sequence"
   $ matrix.info.parameters.required           : Named list()
   $ matrix.organism.parameters.required       : Named list()
   $ matrix.function.parameters.required       : Named list()
   $ matrix.feature.parameters.required        : Named list()
   $ metadata.info.parameters.required         : Named list()
   $ metadata.template.parameters.required     : Named list()
   $ metadata.cv.parameters.required           : Named list()
   $ metadata.ontology.parameters.required     :List of 2
    ..$ version: chr [1:2] "string" "version of ontology to use"
    ..$ name   : chr [1:2] "string" "ontology name"
   $ metadata.export.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ metadata.validate.parameters.required     : Named list()
   $ metagenome.info.parameters.required       : Named list()
   $ metagenome.query.parameters.required      : Named list()
   $ metagenome.instance.parameters.required   :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ profile.info.parameters.required          : Named list()
   $ profile.instance.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ project.info.parameters.required          : Named list()
   $ project.query.parameters.required         : Named list()
   $ project.instance.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ sample.info.parameters.required           : Named list()
   $ sample.query.parameters.required          : Named list()
   $ sample.instance.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ server.info.parameters.required           : Named list()
   $ server.instance.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique server ID"
   $ validation.info.parameters.required       : Named list()
   $ validation.template.parameters.required   :List of 1
    ..$ id: chr [1:2] "string" "SHOCK template id"
   $ validation.data.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "SHOCK data id"
   $ status.info.parameters.required           : Named list()
   $ status.instance.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique process id"
  > doc.MGRAST (3, stratum="required")
  List of 51
   $ annotation.info.parameters.required       : Named list()
   $ annotation.sequence.parameters.required   :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ annotation.similarity.parameters.required :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ compute.info.parameters.required          : Named list()
   $ compute.alphadiversity.parameters.required:List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ download.info.parameters.required         : Named list()
   $ download.instance.parameters.required     :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ download.setlist.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique metagenome identifier"
   $ inbox.info.parameters.required            : Named list()
   $ inbox.view.parameters.required            :List of 1
    ..$ auth: chr [1:2] "string" "unique string of text generated by MG-RAST for your account"
   $ library.info.parameters.required          : Named list()
   $ library.query.parameters.required         : Named list()
   $ library.instance.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ m5nr.info.parameters.required             : Named list()
   $ m5nr.ontology.parameters.required         : Named list()
   $ m5nr.taxonomy.parameters.required         : Named list()
   $ m5nr.sources.parameters.required          : Named list()
   $ m5nr.accession.parameters.required        :List of 1
    ..$ id: chr [1:2] "string" "unique identifier from source DB"
   $ m5nr.alias.parameters.required            :List of 1
    ..$ text: chr [1:2] "string" "text string of partial alias"
   $ m5nr.md5.parameters.required              :List of 1
    ..$ id: chr [1:2] "string" "unique identifier in form of md5 checksum"
   $ m5nr.function.parameters.required         :List of 1
    ..$ text: chr [1:2] "string" "text string of partial function name"
   $ m5nr.organism.parameters.required         :List of 1
    ..$ text: chr [1:2] "string" "text string of partial organism name"
   $ m5nr.sequence.parameters.required         :List of 1
    ..$ text: chr [1:2] "string" "text string of protein sequence"
   $ matrix.info.parameters.required           : Named list()
   $ matrix.organism.parameters.required       : Named list()
   $ matrix.function.parameters.required       : Named list()
   $ matrix.feature.parameters.required        : Named list()
   $ metadata.info.parameters.required         : Named list()
   $ metadata.template.parameters.required     : Named list()
   $ metadata.cv.parameters.required           : Named list()
   $ metadata.ontology.parameters.required     :List of 2
    ..$ version: chr [1:2] "string" "version of ontology to use"
    ..$ name   : chr [1:2] "string" "ontology name"
   $ metadata.export.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ metadata.validate.parameters.required     : Named list()
   $ metagenome.info.parameters.required       : Named list()
   $ metagenome.query.parameters.required      : Named list()
   $ metagenome.instance.parameters.required   :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ profile.info.parameters.required          : Named list()
   $ profile.instance.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ project.info.parameters.required          : Named list()
   $ project.query.parameters.required         : Named list()
   $ project.instance.parameters.required      :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ sample.info.parameters.required           : Named list()
   $ sample.query.parameters.required          : Named list()
   $ sample.instance.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique object identifier"
   $ server.info.parameters.required           : Named list()
   $ server.instance.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique server ID"
   $ validation.info.parameters.required       : Named list()
   $ validation.template.parameters.required   :List of 1
    ..$ id: chr [1:2] "string" "SHOCK template id"
   $ validation.data.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "SHOCK data id"
   $ status.info.parameters.required           : Named list()
   $ status.instance.parameters.required       :List of 1
    ..$ id: chr [1:2] "string" "unique process id"
  > 
  > doc.MGRAST (stratum="attributes")
  List of 51
   $ annotation.info.attributes       : chr "self"
   $ annotation.sequence.attributes   :List of 1
   $ annotation.similarity.attributes :List of 1
   $ compute.info.attributes          : chr "self"
   $ compute.alphadiversity.attributes:List of 3
   $ download.info.attributes         : chr "self"
   $ download.instance.attributes     :List of 1
   $ download.setlist.attributes      :List of 7
   $ inbox.info.attributes            : chr "self"
   $ inbox.view.attributes            :List of 4
   $ library.info.attributes          : chr "self"
   $ library.query.attributes         :List of 7
   $ library.instance.attributes      :List of 10
   $ m5nr.info.attributes             : chr "self"
   $ m5nr.ontology.attributes         :List of 3
   $ m5nr.taxonomy.attributes         :List of 3
   $ m5nr.sources.attributes          :List of 3
   $ m5nr.accession.attributes        :List of 8
   $ m5nr.alias.attributes            :List of 8
   $ m5nr.md5.attributes              :List of 8
   $ m5nr.function.attributes         :List of 8
   $ m5nr.organism.attributes         :List of 8
   $ m5nr.sequence.attributes         :List of 8
   $ matrix.info.attributes           : chr "self"
   $ matrix.organism.attributes       :List of 14
   $ matrix.function.attributes       :List of 14
   $ matrix.feature.attributes        :List of 14
   $ metadata.info.attributes         : chr "self"
   $ metadata.template.attributes     :List of 4
   $ metadata.cv.attributes           :List of 3
   $ metadata.ontology.attributes     :List of 6
   $ metadata.export.attributes       :List of 5
   $ metadata.validate.attributes     :List of 2
   $ metagenome.info.attributes       : chr "self"
   $ metagenome.query.attributes      :List of 9
   $ metagenome.instance.attributes   :List of 13
   $ profile.info.attributes          : chr "self"
   $ profile.instance.attributes      :List of 12
   $ project.info.attributes          : chr "self"
   $ project.query.attributes         :List of 7
   $ project.instance.attributes      :List of 13
   $ sample.info.attributes           : chr "self"
   $ sample.query.attributes          :List of 7
   $ sample.instance.attributes       :List of 10
   $ server.info.attributes           : chr "self"
   $ server.instance.attributes       :List of 9
   $ validation.info.attributes       : chr "self"
   $ validation.template.attributes   :List of 2
   $ validation.data.attributes       :List of 2
   $ status.info.attributes           : chr "self"
   $ status.instance.attributes       :List of 4
  > doc.MGRAST (2, stratum="attributes")
  List of 51
   $ annotation.info.attributes       : chr "self"
   $ annotation.sequence.attributes   :List of 1
    ..$ streaming text:List of 2
   $ annotation.similarity.attributes :List of 1
    ..$ streaming text:List of 2
   $ compute.info.attributes          : chr "self"
   $ compute.alphadiversity.attributes:List of 3
    ..$ url : chr [1:2] "string" "resource location of this object instance"
    ..$ data: chr [1:2] "float" "alpha diversity value"
    ..$ id  : chr [1:2] "string" "unique metagenome identifier"
   $ download.info.attributes         : chr "self"
   $ download.instance.attributes     :List of 1
    ..$ data: chr [1:2] "file" "requested analysis file"
   $ download.setlist.attributes      :List of 7
    ..$ stage_name: chr [1:2] "string" "name of the stage in processing of this file"
    ..$ file_name : chr [1:2] "string" "name of the analysis file"
    ..$ url       : chr [1:2] "string" "url for retrieving this analysis file"
    ..$ id        : chr [1:2] "string" "unique metagenome identifier"
    ..$ file_id   : chr [1:2] "string" "unique identifier of file in stage"
    ..$ stage_type: chr [1:2] "string" "type of the analysis file within a stage, i.e. passed or removed for quality control steps"
    ..$ stage_id  : chr [1:2] "string" "three digit numerical identifier of the stage"
   $ inbox.info.attributes            : chr "self"
   $ inbox.view.attributes            :List of 4
    ..$ timestamp: chr [1:2] "string" "timestamp for return of this query"
    ..$ files    :List of 2
    ..$ url      : chr [1:2] "uri" "resource location of this object instance"
    ..$ id       : chr [1:2] "string" "user login"
   $ library.info.attributes          : chr "self"
   $ library.query.attributes         :List of 7
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ data       :List of 2
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
   $ library.instance.attributes      :List of 10
    ..$ version     : chr [1:2] "integer" "version of the object"
    ..$ project     : chr [1:2] "reference project" "reference to the project object"
    ..$ name        : chr [1:2] "string" "human readable identifier"
    ..$ sequencesets:List of 2
    ..$ metagenome  : chr [1:2] "reference metagenome" "reference to the related metagenome object"
    ..$ created     : chr [1:2] "date" "time the object was first created"
    ..$ url         : chr [1:2] "uri" "resource location of this object instance"
    ..$ id          : chr [1:2] "string" "unique object identifier"
    ..$ sample      : chr [1:2] "reference sample" "reference to the related sample object"
    ..$ metadata    : chr [1:2] "hash" "key value pairs describing metadata"
   $ m5nr.info.attributes             : chr "self"
   $ m5nr.ontology.attributes         :List of 3
    ..$ version: chr [1:2] "integer" "version of M5NR"
    ..$ url    : chr [1:2] "uri" "resource location of this object instance"
    ..$ data   :List of 2
   $ m5nr.taxonomy.attributes         :List of 3
    ..$ version: chr [1:2] "integer" "version of M5NR"
    ..$ url    : chr [1:2] "uri" "resource location of this object instance"
    ..$ data   :List of 2
   $ m5nr.sources.attributes          :List of 3
    ..$ version: chr [1:2] "integer" "version of M5NR"
    ..$ url    : chr [1:2] "uri" "resource location of this object instance"
    ..$ data   :List of 2
   $ m5nr.accession.attributes        :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.alias.attributes            :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.md5.attributes              :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.function.attributes         :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.organism.attributes         :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.sequence.attributes         :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ matrix.info.attributes           : chr "self"
   $ matrix.organism.attributes       :List of 14
    ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date                : chr [1:2] "date" "time the output data was generated"
    ..$ data                :List of 2
    ..$ rows                :List of 2
    ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url          : chr [1:2] "string" "url to the format specification"
    ..$ format              : chr [1:2] "string" "format specification name"
    ..$ columns             :List of 2
    ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    ..$ shape               :List of 2
    ..$ id                  : chr [1:2] "string" "unique object identifier"
    ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ matrix.function.attributes       :List of 14
    ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date                : chr [1:2] "date" "time the output data was generated"
    ..$ data                :List of 2
    ..$ rows                :List of 2
    ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url          : chr [1:2] "string" "url to the format specification"
    ..$ format              : chr [1:2] "string" "format specification name"
    ..$ columns             :List of 2
    ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    ..$ shape               :List of 2
    ..$ id                  : chr [1:2] "string" "unique object identifier"
    ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ matrix.feature.attributes        :List of 14
    ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date                : chr [1:2] "date" "time the output data was generated"
    ..$ data                :List of 2
    ..$ rows                :List of 2
    ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url          : chr [1:2] "string" "url to the format specification"
    ..$ format              : chr [1:2] "string" "format specification name"
    ..$ columns             :List of 2
    ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    ..$ shape               :List of 2
    ..$ id                  : chr [1:2] "string" "unique object identifier"
    ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ metadata.info.attributes         : chr "self"
   $ metadata.template.attributes     :List of 4
    ..$ ep     :List of 2
    ..$ project:List of 2
    ..$ library:List of 2
    ..$ sample :List of 2
   $ metadata.cv.attributes           :List of 3
    ..$ ontology:List of 2
    ..$ ont_info:List of 2
    ..$ select  :List of 2
   $ metadata.ontology.attributes     :List of 6
    ..$ version : chr [1:2] "string" "version of this ontology"
    ..$ rootNode: chr [1:2] "string" "ontology ID of root"
    ..$ name    : chr [1:2] "string" "ontology name"
    ..$ type    : chr [1:2] "string" "this type"
    ..$ showRoot: chr [1:2] "boolean" "option to show root when displaying"
    ..$ nodes   :List of 2
   $ metadata.export.attributes       :List of 5
    ..$ sampleNum: chr [1:2] "int" "number of samples in project"
    ..$ samples  :List of 2
    ..$ name     : chr [1:2] "string" "human readable identifier"
    ..$ data     :List of 2
    ..$ id       : chr [1:2] "string" "unique object identifier"
   $ metadata.validate.attributes     :List of 2
    ..$ message : chr [1:2] "string" "if not valid, reason why"
    ..$ is_valid: chr [1:2] "boolean" "the inputed value is valid for the given category and label"
   $ metagenome.info.attributes       : chr "self"
   $ metagenome.query.attributes      :List of 9
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of the object"
    ..$ data       :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ metagenome.instance.attributes   :List of 13
    ..$ statistics   : chr [1:2] "hash" "key value pairs describing statistics"
    ..$ status       :List of 2
    ..$ version      : chr [1:2] "integer" "version of the metagenome"
    ..$ project      : chr [1:2] "reference project" "reference to the project object"
    ..$ name         : chr [1:2] "string" "name of metagenome"
    ..$ sequence_type: chr [1:2] "string" "sequencing type"
    ..$ library      : chr [1:2] "reference library" "reference to the related library object"
    ..$ created      : chr [1:2] "date" "time the metagenome was first created"
    ..$ url          : chr [1:2] "uri" "resource location of this object instance"
    ..$ id           : chr [1:2] "string" "unique metagenome identifier"
    ..$ sample       : chr [1:2] "reference sample" "reference to the related sample object"
    ..$ metadata     : chr [1:2] "hash" "key value pairs describing all metadata"
    ..$ mixs         : chr [1:2] "hash" "key value pairs describing MIxS metadata"
   $ profile.info.attributes          : chr "self"
   $ profile.instance.attributes      :List of 12
    ..$ generated_by       : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type        : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date               : chr [1:2] "date" "time the output data was generated"
    ..$ data               :List of 2
    ..$ rows               :List of 2
    ..$ matrix_element_type: chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url         : chr [1:2] "string" "url to the format specification"
    ..$ format             : chr [1:2] "string" "format specification name"
    ..$ columns            :List of 2
    ..$ id                 : chr [1:2] "string" "unique object identifier"
    ..$ type               : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
    ..$ shape              :List of 2
   $ project.info.attributes          : chr "self"
   $ project.query.attributes         :List of 7
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ data       :List of 2
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
   $ project.instance.attributes      :List of 13
    ..$ status        :List of 2
    ..$ version       : chr [1:2] "integer" "version of the object"
    ..$ name          : chr [1:2] "string" "human readable identifier"
    ..$ description   : chr [1:2] "string" "a short, comprehensive description of the project"
    ..$ metagenomes   :List of 2
    ..$ libraries     :List of 2
    ..$ created       : chr [1:2] "date" "time the object was first created"
    ..$ samples       :List of 2
    ..$ funding_source: chr [1:2] "string" "the official name of the source of funding of this project"
    ..$ url           : chr [1:2] "uri" "resource location of this object instance"
    ..$ metadata      : chr [1:2] "hash" "key value pairs describing metadata"
    ..$ id            : chr [1:2] "string" "unique object identifier"
    ..$ pi            : chr [1:2] "string" "the first and last name of the principal investigator of the project"
   $ sample.info.attributes           : chr "self"
   $ sample.query.attributes          :List of 7
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ data       :List of 2
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
   $ sample.instance.attributes       :List of 10
    ..$ version    : chr [1:2] "integer" "version of the object"
    ..$ project    : chr [1:2] "reference project" "reference to the project of this sample"
    ..$ name       : chr [1:2] "string" "human readable identifier"
    ..$ metagenomes:List of 2
    ..$ libraries  :List of 2
    ..$ created    : chr [1:2] "date" "time the object was first created"
    ..$ env_package:List of 2
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ id         : chr [1:2] "string" "unique object identifier"
    ..$ metadata   : chr [1:2] "hash" "key value pairs describing metadata"
   $ server.info.attributes           : chr "self"
   $ server.instance.attributes       :List of 9
    ..$ info              : chr [1:2] "string" "informational text, i.e. downtime warnings"
    ..$ basepairs         : chr [1:2] "integer" "total number of basepairs"
    ..$ status            : chr [1:2] "string" "status of the server"
    ..$ version           : chr [1:2] "string" "version number of the server"
    ..$ url               : chr [1:2] "uri" "resource location of this object instance"
    ..$ id                : chr [1:2] "string" "unique identifier of this server"
    ..$ public_metagenomes: chr [1:2] "integer" "total number of public metagenomes"
    ..$ metagenomes       : chr [1:2] "integer" "total number of metagenomes"
    ..$ sequences         : chr [1:2] "integer" "total number of sequences"
   $ validation.info.attributes       : chr "self"
   $ validation.template.attributes   :List of 2
    ..$ error:List of 2
    ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
   $ validation.data.attributes       :List of 2
    ..$ error:List of 2
    ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
   $ status.info.attributes           : chr "self"
   $ status.instance.attributes       :List of 4
    ..$ status:List of 3
    ..$ url   : chr [1:2] "url" "resource location of this object instance"
    ..$ data  : chr [1:2] "hash" "if status is done, data holds the result, otherwise data is not present"
    ..$ id    : chr [1:2] "integer" "process id"
  > doc.MGRAST (3, stratum="attributes")
  List of 51
   $ annotation.info.attributes       : chr "self"
   $ annotation.sequence.attributes   :List of 1
    ..$ streaming text:List of 2
    .. ..$ : chr "object"
    .. ..$ :List of 2
   $ annotation.similarity.attributes :List of 1
    ..$ streaming text:List of 2
    .. ..$ : chr "object"
    .. ..$ :List of 2
   $ compute.info.attributes          : chr "self"
   $ compute.alphadiversity.attributes:List of 3
    ..$ url : chr [1:2] "string" "resource location of this object instance"
    ..$ data: chr [1:2] "float" "alpha diversity value"
    ..$ id  : chr [1:2] "string" "unique metagenome identifier"
   $ download.info.attributes         : chr "self"
   $ download.instance.attributes     :List of 1
    ..$ data: chr [1:2] "file" "requested analysis file"
   $ download.setlist.attributes      :List of 7
    ..$ stage_name: chr [1:2] "string" "name of the stage in processing of this file"
    ..$ file_name : chr [1:2] "string" "name of the analysis file"
    ..$ url       : chr [1:2] "string" "url for retrieving this analysis file"
    ..$ id        : chr [1:2] "string" "unique metagenome identifier"
    ..$ file_id   : chr [1:2] "string" "unique identifier of file in stage"
    ..$ stage_type: chr [1:2] "string" "type of the analysis file within a stage, i.e. passed or removed for quality control steps"
    ..$ stage_id  : chr [1:2] "string" "three digit numerical identifier of the stage"
   $ inbox.info.attributes            : chr "self"
   $ inbox.view.attributes            :List of 4
    ..$ timestamp: chr [1:2] "string" "timestamp for return of this query"
    ..$ files    :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ url      : chr [1:2] "uri" "resource location of this object instance"
    ..$ id       : chr [1:2] "string" "user login"
   $ library.info.attributes          : chr "self"
   $ library.query.attributes         :List of 7
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
   $ library.instance.attributes      :List of 10
    ..$ version     : chr [1:2] "integer" "version of the object"
    ..$ project     : chr [1:2] "reference project" "reference to the project object"
    ..$ name        : chr [1:2] "string" "human readable identifier"
    ..$ sequencesets:List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "reference sequenceset" "a list of references to the related sequence sets"
    ..$ metagenome  : chr [1:2] "reference metagenome" "reference to the related metagenome object"
    ..$ created     : chr [1:2] "date" "time the object was first created"
    ..$ url         : chr [1:2] "uri" "resource location of this object instance"
    ..$ id          : chr [1:2] "string" "unique object identifier"
    ..$ sample      : chr [1:2] "reference sample" "reference to the related sample object"
    ..$ metadata    : chr [1:2] "hash" "key value pairs describing metadata"
   $ m5nr.info.attributes             : chr "self"
   $ m5nr.ontology.attributes         :List of 3
    ..$ version: chr [1:2] "integer" "version of M5NR"
    ..$ url    : chr [1:2] "uri" "resource location of this object instance"
    ..$ data   :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
   $ m5nr.taxonomy.attributes         :List of 3
    ..$ version: chr [1:2] "integer" "version of M5NR"
    ..$ url    : chr [1:2] "uri" "resource location of this object instance"
    ..$ data   :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
   $ m5nr.sources.attributes          :List of 3
    ..$ version: chr [1:2] "integer" "version of M5NR"
    ..$ url    : chr [1:2] "uri" "resource location of this object instance"
    ..$ data   :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "object" "source object"
   $ m5nr.accession.attributes        :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.alias.attributes            :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.md5.attributes              :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.function.attributes         :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.organism.attributes         :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ m5nr.sequence.attributes         :List of 8
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of M5NR"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ matrix.info.attributes           : chr "self"
   $ matrix.organism.attributes       :List of 14
    ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date                : chr [1:2] "date" "time the output data was generated"
    ..$ data                :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ rows                :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url          : chr [1:2] "string" "url to the format specification"
    ..$ format              : chr [1:2] "string" "format specification name"
    ..$ columns             :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    ..$ shape               :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
    ..$ id                  : chr [1:2] "string" "unique object identifier"
    ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ matrix.function.attributes       :List of 14
    ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date                : chr [1:2] "date" "time the output data was generated"
    ..$ data                :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ rows                :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url          : chr [1:2] "string" "url to the format specification"
    ..$ format              : chr [1:2] "string" "format specification name"
    ..$ columns             :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    ..$ shape               :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
    ..$ id                  : chr [1:2] "string" "unique object identifier"
    ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ matrix.feature.attributes        :List of 14
    ..$ generated_by        : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type         : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date                : chr [1:2] "date" "time the output data was generated"
    ..$ data                :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ rows                :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
    ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url          : chr [1:2] "string" "url to the format specification"
    ..$ format              : chr [1:2] "string" "format specification name"
    ..$ columns             :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ url                 : chr [1:2] "uri" "resource location of this object instance"
    ..$ shape               :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
    ..$ id                  : chr [1:2] "string" "unique object identifier"
    ..$ type                : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
   $ metadata.info.attributes         : chr "self"
   $ metadata.template.attributes     :List of 4
    ..$ ep     :List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
    ..$ project:List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
    ..$ library:List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
    ..$ sample :List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
   $ metadata.cv.attributes           :List of 3
    ..$ ontology:List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
    ..$ ont_info:List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
    ..$ select  :List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
   $ metadata.ontology.attributes     :List of 6
    ..$ version : chr [1:2] "string" "version of this ontology"
    ..$ rootNode: chr [1:2] "string" "ontology ID of root"
    ..$ name    : chr [1:2] "string" "ontology name"
    ..$ type    : chr [1:2] "string" "this type"
    ..$ showRoot: chr [1:2] "boolean" "option to show root when displaying"
    ..$ nodes   :List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
   $ metadata.export.attributes       :List of 5
    ..$ sampleNum: chr [1:2] "int" "number of samples in project"
    ..$ samples  :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "object" "sample object containing sample metadata, sample libraries, sample envPackage"
    ..$ name     : chr [1:2] "string" "human readable identifier"
    ..$ data     :List of 2
    .. ..$ : chr "hash"
    .. ..$ :List of 2
    ..$ id       : chr [1:2] "string" "unique object identifier"
   $ metadata.validate.attributes     :List of 2
    ..$ message : chr [1:2] "string" "if not valid, reason why"
    ..$ is_valid: chr [1:2] "boolean" "the inputed value is valid for the given category and label"
   $ metagenome.info.attributes       : chr "self"
   $ metagenome.query.attributes      :List of 9
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ version    : chr [1:2] "integer" "version of the object"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
   $ metagenome.instance.attributes   :List of 13
    ..$ statistics   : chr [1:2] "hash" "key value pairs describing statistics"
    ..$ status       :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ version      : chr [1:2] "integer" "version of the metagenome"
    ..$ project      : chr [1:2] "reference project" "reference to the project object"
    ..$ name         : chr [1:2] "string" "name of metagenome"
    ..$ sequence_type: chr [1:2] "string" "sequencing type"
    ..$ library      : chr [1:2] "reference library" "reference to the related library object"
    ..$ created      : chr [1:2] "date" "time the metagenome was first created"
    ..$ url          : chr [1:2] "uri" "resource location of this object instance"
    ..$ id           : chr [1:2] "string" "unique metagenome identifier"
    ..$ sample       : chr [1:2] "reference sample" "reference to the related sample object"
    ..$ metadata     : chr [1:2] "hash" "key value pairs describing all metadata"
    ..$ mixs         : chr [1:2] "hash" "key value pairs describing MIxS metadata"
   $ profile.info.attributes          : chr "self"
   $ profile.instance.attributes      :List of 12
    ..$ generated_by       : chr [1:2] "string" "identifier of the data generator"
    ..$ matrix_type        : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
    ..$ date               : chr [1:2] "date" "time the output data was generated"
    ..$ data               :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ rows               :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ matrix_element_type: chr [1:2] "string" "data type of the elements in the return matrix"
    ..$ format_url         : chr [1:2] "string" "url to the format specification"
    ..$ format             : chr [1:2] "string" "format specification name"
    ..$ columns            :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ id                 : chr [1:2] "string" "unique object identifier"
    ..$ type               : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
    ..$ shape              :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
   $ project.info.attributes          : chr "self"
   $ project.query.attributes         :List of 7
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
   $ project.instance.attributes      :List of 13
    ..$ status        :List of 2
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ version       : chr [1:2] "integer" "version of the object"
    ..$ name          : chr [1:2] "string" "human readable identifier"
    ..$ description   : chr [1:2] "string" "a short, comprehensive description of the project"
    ..$ metagenomes   :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "reference metagenome" "a list of references to the related metagenome objects"
    ..$ libraries     :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "reference library" "a list of references to the related library objects"
    ..$ created       : chr [1:2] "date" "time the object was first created"
    ..$ samples       :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "reference sample" "a list of references to the related sample objects"
    ..$ funding_source: chr [1:2] "string" "the official name of the source of funding of this project"
    ..$ url           : chr [1:2] "uri" "resource location of this object instance"
    ..$ metadata      : chr [1:2] "hash" "key value pairs describing metadata"
    ..$ id            : chr [1:2] "string" "unique object identifier"
    ..$ pi            : chr [1:2] "string" "the first and last name of the principal investigator of the project"
   $ sample.info.attributes           : chr "self"
   $ sample.query.attributes          :List of 7
    ..$ next       : chr [1:2] "uri" "link to the previous set or null if this is the first set"
    ..$ prev       : chr [1:2] "uri" "link to the next set or null if this is the last set"
    ..$ order      : chr [1:2] "string" "name of the attribute the returned data is ordered by"
    ..$ limit      : chr [1:2] "integer" "maximum number of data items returned, default is 10"
    ..$ data       :List of 2
    .. ..$ : chr "list"
    .. ..$ :List of 2
    ..$ offset     : chr [1:2] "integer" "zero based index of the first returned data item"
    ..$ total_count: chr [1:2] "integer" "total number of available data items"
   $ sample.instance.attributes       :List of 10
    ..$ version    : chr [1:2] "integer" "version of the object"
    ..$ project    : chr [1:2] "reference project" "reference to the project of this sample"
    ..$ name       : chr [1:2] "string" "human readable identifier"
    ..$ metagenomes:List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "reference metagenome" "a list of references to the related metagenome objects"
    ..$ libraries  :List of 2
    .. ..$ : chr "list"
    .. ..$ : chr [1:2] "reference library" "a list of references to the related library objects"
    ..$ created    : chr [1:2] "date" "time the object was first created"
    ..$ env_package:List of 2
    .. ..$ : chr "object"
    .. ..$ :List of 2
    ..$ url        : chr [1:2] "uri" "resource location of this object instance"
    ..$ id         : chr [1:2] "string" "unique object identifier"
    ..$ metadata   : chr [1:2] "hash" "key value pairs describing metadata"
   $ server.info.attributes           : chr "self"
   $ server.instance.attributes       :List of 9
    ..$ info              : chr [1:2] "string" "informational text, i.e. downtime warnings"
    ..$ basepairs         : chr [1:2] "integer" "total number of basepairs"
    ..$ status            : chr [1:2] "string" "status of the server"
    ..$ version           : chr [1:2] "string" "version number of the server"
    ..$ url               : chr [1:2] "uri" "resource location of this object instance"
    ..$ id                : chr [1:2] "string" "unique identifier of this server"
    ..$ public_metagenomes: chr [1:2] "integer" "total number of public metagenomes"
    ..$ metagenomes       : chr [1:2] "integer" "total number of metagenomes"
    ..$ sequences         : chr [1:2] "integer" "total number of sequences"
   $ validation.info.attributes       : chr "self"
   $ validation.template.attributes   :List of 2
    ..$ error:List of 2
    .. ..$ : chr "array"
    .. ..$ : chr [1:2] "string" "array of invalid entries"
    ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
   $ validation.data.attributes       :List of 2
    ..$ error:List of 2
    .. ..$ : chr "array"
    .. ..$ : chr [1:2] "string" "array of invalid entries"
    ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
   $ status.info.attributes           : chr "self"
   $ status.instance.attributes       :List of 4
    ..$ status:List of 3
    .. ..$ : chr "string"
    .. ..$ : chr "cv"
    .. ..$ :List of 2
    ..$ url   : chr [1:2] "url" "resource location of this object instance"
    ..$ data  : chr [1:2] "hash" "if status is done, data holds the result, otherwise data is not present"
    ..$ id    : chr [1:2] "integer" "process id"
  > 
  > doc.MGRAST (2, head = c('mat','orga','param','opt','group_level'))
  List of 2
   $ : chr "cv"
   $ :List of 8
    ..$ : chr [1:2] "strain" "bottom organism taxanomic level"
    ..$ : chr [1:2] "species" "organism type level"
    ..$ : chr [1:2] "genus" "organism taxanomic level"
    ..$ : chr [1:2] "family" "organism taxanomic level"
    ..$ : chr [1:2] "order" "organism taxanomic level"
    ..$ : chr [1:2] "class" "organism taxanomic level"
    ..$ : chr [1:2] "phylum" "organism taxanomic level"
    ..$ : chr [1:2] "domain" "top organism taxanomic level"
  > doc.MGRAST (2, head = c('mat','func','param','opt','group_level'))
  List of 2
   $ : chr "cv"
   $ :List of 4
    ..$ : chr [1:2] "function" "bottom function ontology level"
    ..$ : chr [1:2] "level3" "function ontology level"
    ..$ : chr [1:2] "level2" "function ontology level"
    ..$ : chr [1:2] "level1" "top function ontology level"
  > 
  > #-----------------------------------------------------------------------------
  > #  test URL construction from arguments, without issuing any calls.
  > #
  > #  the first set are calls from API documentation, adapted by hand, April 2014.
  > #  some are copied in the doc examples of call.MGRAST() and parse.MGRAST().
  > #  if these are updated, so should those be.  (see above for the original URLs.)
  > #
  > #  the second set are test cases put together by hand.
  > #  calls intended to produce errors are "try"d.
  > #-----------------------------------------------------------------------------
  > 
  > call.MGRAST ('an', 'se', id=4447943.3, ev=10, ty='or', so='Sw', destfile="no.file", issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
  > call.MGRAST ('an', 'si', id=4447943.3, iden=80, ty='fu', so='KO', destfile="no.file", issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO"
  > call.MGRAST ('co', 'al', id=4447943.3, le='or', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/compute/alphadiversity/mgm4447943.3?level=order"
  > call.MGRAST ('do', 'ins', id=4447943.3, fi=350.1, destfile="no.file", issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/download/mgm4447943.3?file=350.1"
  > call.MGRAST ('do', 'se', id=4447943.3, st=650, issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/download/mgm4447943.3?stage=650"
  > call.MGRAST ('li', 'qu', li=20, or='na', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/library?limit=20&order=name"
  > call.MGRAST ('li', 'ins', id=52924, ve='fu', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/library/mgl52924?verbosity=full"
  > call.MGRAST ('m5', 'on', so='Subsystems', mi='level3', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/ontology?source=Subsystems&min_level=level3"
  > call.MGRAST ('m5', 'ta', filter='Bacteroidetes', filter_l='phylum', mi='genus', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus"
  > call.MGRAST ('m5', 'so', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/sources"
  > call.MGRAST ('m5', 'ac', id='YP_003268079.1', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/accession/YP_003268079.1"
  > call.MGRAST ('m5', 'al', text='IPR001478', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/alias/IPR001478"
  > call.MGRAST ('m5', 'md', id='000821a2e2f63df1a3873e4b280002a8', so='InterPro', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro"
  > call.MGRAST ('m5', 'fu', text='sulfatase', so='GenBank', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/function/sulfatase?source=GenBank"
  > call.MGRAST ('m5', 'or', text='akkermansia', so='KEGG', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/organism/akkermansia?source=KEGG"
  > call.MGRAST ('m5', 'se', text='MAGENHQWQGSIL', so='TrEMBL', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL"
  > call.MGRAST ('ma', 'or', id=c(4447943.3, 4447192.3, 4447102.3, 4447103.3), gro='family', so='Ref', resu='ab', ev=15, issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=family&source=RefSeq&result_type=abundance&evalue=15"
  > call.MGRAST ('ma', 'fu', id=c(4447943.3, 4447192.3, 4447102.3, 4447103.3), gro='level3', so='Sub', resu='ab', iden=80, filter_l='phylum', filter='Firmicutes', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=level3&source=Subsystems&result_type=abundance&identity=80&filter_level=phylum&filter=Firmicutes"
  > call.MGRAST ('ma', 'fe', id=c(4447943.3, 4447192.3, 4447102.3, 4447103.3), so='KE', resu='ev', len=25, issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&source=KEGG&result_type=evalue&length=25"
  > call.MGRAST ('metadata', 'te', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/metadata/template"
  > call.MGRAST ('metadata', 'cv', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/metadata/cv"
  > call.MGRAST ('metadata', 'ex', id=128, issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/metadata/export/128"
  > call.MGRAST ('metageno','qu', li=20, ord='name', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/metagenome?limit=20&order=name"
  > call.MGRAST ('metageno','ins', id=4447943.3, ve='me', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/metagenome/mgm4447943.3?verbosity=metadata"
  > call.MGRAST ('proj', 'qu', li=20, or='na', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/project?limit=20&order=name"
  > call.MGRAST ('proj', 'ins', id=128, ve='fu', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/project/mgp128?verbosity=full"
  > call.MGRAST ('sa', 'qu', li=20, or='na', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/sample?limit=20&order=name"
  > call.MGRAST ('sa', 'ins', id=25823, ve='fu', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/sample/mgs25823?verbosity=full"
  > call.MGRAST ('va', 'te', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/validation/template"
  > call.MGRAST ('va', 'da', issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/validation/data"
  > 
  > try (call.MGRAST ("ann", issue=FALSE))
  Error in match.arg(request, names(api.root[[resource]])) : 
    argument "request" is missing, with no default
  > try (call.MGRAST ("ann", "seque", issue=FALSE))
  Error in call.MGRAST("ann", "seque", issue = FALSE) : 
    an output file should be specified for this request
  > call.MGRAST ("ann", "seque", destfile="no.file", issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/annotation/sequence"
  > call.MGRAST ("compu", "alpha", issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/compute/alphadiversity"
  > call.MGRAST ("downloa", "setl", issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/download"
  > call.MGRAST ("downloa", "setl", id=5, issue=FALSE)
  [1] "http://api.metagenomics.anl.gov/1/download/mgm5"
  > try (call.MGRAST ("downloa", "sel", id=5, issue=FALSE))
  Error in match.arg(request, names(api.root[[resource]])) : 
    'arg' should be one of "info", "instance", "setlist"
  > call.MGRAST ("download", "setlist", st=5, id=10, i=11, issue=FALSE)
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  MGRASTer
   --- call from context --- 
  paste(c(get("server", .MGRAST), get("API.version", .MGRAST), 
      resource, if (length(request) && resource %in% c("annotation", 
          "compute", "inbox", "m5nr", "matrix", "metadata", "validation")) request, 
      if (length(required.str) && nchar(required.str)) required.str), 
      collapse = "/")
   --- call from argument --- 
  length(required.str) && nchar(required.str)
   --- R stacktrace ---
  where 1: paste(c(get("server", .MGRAST), get("API.version", .MGRAST), 
      resource, if (length(request) && resource %in% c("annotation", 
          "compute", "inbox", "m5nr", "matrix", "metadata", "validation")) request, 
      if (length(required.str) && nchar(required.str)) required.str), 
      collapse = "/")
  where 2: call.MGRAST("download", "setlist", st = 5, id = 10, i = 11, issue = FALSE)
  
   --- value of length: 2 type: integer ---
  [1] 5 5
   --- function from context --- 
  function (..., sep = " ", collapse = NULL, recycle0 = FALSE) 
  .Internal(paste(list(...), sep, collapse, recycle0))
  <bytecode: 0xfd3318>
  <environment: namespace:base>
   --- function search by body ---
  Function paste in namespace base has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/MGRASTer.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:31.24, 31.47 + 6.12