@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix Dirent: .
@prefix cwl: .
@prefix ResourceRequirement: .
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-n l//" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
sld:type cwl:Directory .
cwl:in , ;
cwl:out , ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:prefix
"-seqids" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:default ".xml" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--additional-suffix=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
cwl:source .
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type xsd:string .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "file concatenation" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "cat" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:stdout "cat.out" .
cwl:inputBinding [ CommandLineBinding:prefix
"-aligns" ] ;
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
rdfs:label "spurious_annot" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:source .
cwl:default "output.asn" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:Directory .
cwl:default "output" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-O" ] ;
sld:type xsd:string , sld:null .
cwl:default "*" .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "reduce" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-nogenbank" ) ;
cwl:baseCommand ( "reduce" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs .
sld:type cwl:File .
rdfs:label "Search AntiFam I" ;
cwl:in , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type cwl:Directory .
cwl:in , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
cwl:outputBinding [ CommandOutputBinding:glob
"cat.out" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:default "protein.seqids" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-oseqids" ] ;
sld:type xsd:string .
sld:type cwl:Directory .
a cwl:CommandLineTool ;
rdfs:label "hmmsearch_create_jobs" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-no-merge-hmms" ) ;
cwl:baseCommand ( "hmmsearch_create_jobs" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.hmm_path)"
]
] .
sld:type cwl:File .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-hmmsearch-path" ] ;
sld:type xsd:string , sld:null .
cwl:source .
sld:type cwl:Directory .
sld:type cwl:Directory .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:label "hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs .
sld:type cwl:Directory .
cwl:in , , , , , , ;
cwl:out ;
cwl:run .
sld:type cwl:Directory .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.mask)?*$(inputs.suffix)" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"-asn-cache" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "gpx_qdump" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "gpx_qdump" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-unzip" ] ;
sld:type xsd:string , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "hmmsearch_wnode" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ;
cwl:baseCommand ( "hmmsearch_wnode" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMax 3000
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.asn_cache)"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.proteins)"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.hmm_path)"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.workdir)"
] ;
cwl:listing [ cwl:entry "${ var blob = '# fam.mft created for hmmsearch_wnode from input hmms_tab File\\n'; if ( inputs.hmms_tab == null ) { return blob; } else { return blob + inputs.hmms_tab.path; } }" ;
cwl:entryname "fam.mft"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
rdfs:label "AntiFam tainted proteins I" ;
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-path" ] ;
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:prefix
"-lds2" ] ;
sld:type cwl:File .
cwl:default "jobs.xml" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
cwl:default "workpath" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-workpath" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:prefix
"-hmm-path" ] ;
sld:type cwl:Directory .
cwl:default "hmm_hits.asn" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.workpath)" ] ;
sld:type cwl:Directory .
cwl:source