@prefix LoadListingRequirement: .
@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:outputBinding [ CommandOutputBinding:glob
"alpha_diversity.txt" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "Path to reference sequences. For assignment with\nblast, these are used to generate a blast database.\nFor assignment with rdp, they are used as training\nsequences for the classifier. [default:\n/usr/local/lib/python2.7/dist-packages/qiime_default_r\n" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--reference_seqs_fp" ] ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"taxonomy" ] ;
sld:type cwl:Directory .
sld:type cwl:File .
cwl:default "otu-table-filtered-samples.biom" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output_fp" ] ;
sld:type xsd:string .
sld:type .
cwl:default 2 ;
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"filter_samples_from_otu_table.error" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"otus/uclust_picked_otus/*_otus.txt" ] ;
sld:type cwl:File , sld:null .
cwl:default 7 , 6 , 5 , 4 , 3 , 2 ;
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:prefix "--level"
] ;
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"otus/rep_set.tre" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:prefix "-o" ;
cwl:valueFrom "alpha_diversity.txt"
]
) ;
cwl:baseCommand ( "alpha_diversity.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "alpha_diversity.error" ;
cwl:stdout "alpha_diversity.out" ;
ns1:copyrightHolder "n/a" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "summarize_taxa.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:inputs , , , ;
cwl:outputs , , , , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "summarize_taxa.error" ;
cwl:stdout "summarize_taxa.out" .
cwl:inputBinding [ CommandLineBinding:prefix
"-m" ] ;
sld:type cwl:File .
cwl:default "PD_whole_tree" , "chao1" , "observed_otus" , "shannon" .
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
cwl:source ;
cwl:valueFrom "${ \n self.forEach( element => {\n var res = element.location.match(/_L(\\d+)/);\n element.pos = res[1]\n } );\n return self.sort(function(a,b){ return a.pos - b.pos } )\n}\n" .
rdfs:label "make out table" ;
cwl:in , ;
cwl:out , ;
cwl:run .
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"otu_table.biom" ] ;
sld:type cwl:File .
cwl:default 100 ;
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--tree_path" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"assign_taxonomy.out" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"plot_taxa_summary.out" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"alpha_diversity.error" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"pick_de_novo_otus.error" ] ;
sld:type cwl:File .
cwl:source .
rdfs:label "sort otu table by samples" ;
cwl:in , ;
cwl:out , ;
cwl:run .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "sort_otu_table.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "sort_otu_table.error" ;
cwl:stdout "sort_otu_table.out" .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:prefix "--output_biom_fp" ;
cwl:valueFrom "otu_table.biom"
]
) ;
cwl:baseCommand ( "make_otu_table.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "make_otu_table.error" ;
cwl:stdout "make_otu_table.out" .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--absolute_abundance" ] ;
sld:type xsd:boolean .
cwl:inputBinding [ CommandLineBinding:prefix
"-i" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"sort_otu_table.out" ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.labels)" .
cwl:source .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:prefix "--output_dir" ;
cwl:valueFrom "taxonomy"
]
) ;
cwl:baseCommand ( "assign_taxonomy.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "assign_taxonomy.error" ;
cwl:stdout "assign_taxonomy.out" ;
ns1:copyrightHolder "n/a" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)/*.biom" ] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"make_otu_table.out" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"otus/uclust_assigned_taxonomy/*_rep_set_tax_assignments.txt" ] ;
sld:type cwl:File , sld:null .
rdfs:label "alpha diversity" ;
cwl:in , , ;
cwl:out , ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"filter_otus_from_otu_table.out" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"otus" ] ;
sld:type cwl:Directory .
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"beta_diversity_through_plots.out" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:Directory .
rdfs:comment "Input OTU table filepath in BIOM format" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input_otu_table" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( "-s"
[ CommandLineBinding:prefix "--chart_type" ;
cwl:valueFrom "pie,area,bar"
]
) ;
cwl:baseCommand ( "plot_taxa_summary.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "plot_taxa_summary.error" ;
cwl:stdout "plot_taxa_summary.out" .
cwl:source .
rdfs:label "list taxonomic levels" ;
cwl:in , ;
cwl:out , , , ;
cwl:run .
cwl:default 0 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min_count" ] ;
sld:type xsd:int .
sld:symbols , , , , , , ;
sld:type sld:enum .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "filter_otus_from_otu_table.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "filter_otus_from_otu_table.error" ;
cwl:stdout "filter_otus_from_otu_table.out" ;
ns1:copyrightHolder "n/a" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" .
rdfs:comment "Error logs for each step, collected by default and can be empty." ;
cwl:outputSource , , , , , , , , ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"filter_samples_from_otu_table.out" ] ;
sld:type cwl:File .
sld:symbols , , , , , , ;
sld:type sld:enum .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:Directory .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "filter_samples_from_otu_table.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/qiime:1.0.20180919"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "qiime" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_008249" ;
SoftwarePackage:version "1.9.1"
]
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:ramMin 1024
] ;
cwl:stderr "filter_samples_from_otu_table.error" ;
cwl:stdout "filter_samples_from_otu_table.out" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)/*.txt" ] ;
sld:type [ sld:items cwl:File , sld:null ;
sld:type sld:array
] .
rdfs:comment "fasta file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input_fp" ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.tree)" .
cwl:outputBinding [ CommandOutputBinding:glob
"summarize_taxa.error" ] ;
sld:type cwl:File .
rdfs:label "beta diversity" ;
cwl:in , , ;
cwl:out , , ;
cwl:run .
rdfs:label "plot summaries" ;
cwl:in , ;
cwl:out , ;
cwl:run .
cwl:source .
rdfs:comment "fasta file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input_fasta_fp" ] ;
sld:type cwl:File .
rdfs:comment "Input OTU table filepath in BIOM format" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input_fp" ] ;
sld:type cwl:File .
rdfs:comment "cluster ID to sequence IDs mapping, two column" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--otu_map_fp" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"alpha_diversity.out" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"pick_de_novo_otus.out" ] ;
sld:type cwl:File .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:outputSource , , , , , , ;
sld:type [ sld:items cwl:Directory , cwl:File ;
sld:type sld:array
] .
rdfs:comment "Path to tab-delimited file mapping sequences to\nassigned taxonomy. Each assigned taxonomy is provided\nas a semicolon-separated list. For assignment with\nrdp, each assigned taxonomy must be exactly 6 levels\ndeep. [default: /usr/local/lib/python2.7/dist-packages\n/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_\ntaxonomy.txt]\n" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--id_to_taxonomy_fp" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"otus/uclust_picked_otus/*_clusters.uc" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--taxonomy" ] ;
sld:type cwl:File , sld:null .
sld:type [ sld:fields , ;
sld:type sld:record
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:Directory , sld:null .
sld:type [ sld:fields , ;
sld:type sld:record
] .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:prefix "-o" ;
cwl:valueFrom "beta_diversity"
]
) ;
cwl:baseCommand ( "beta_diversity_through_plots.py" ) ;
cwl:cwlVersion