@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: .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-rfam-stockholm" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-path" ] ;
sld:type cwl:Directory .
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-rfam-amendments" ] ;
sld:type cwl:File .
cwl:source .
cwl:default 0 ;
cwl:inputBinding [ CommandLineBinding:prefix
"-cmsearch-cpu" ] ;
sld:type xsd:int , sld:null .
cwl:in , , , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"-ids" ] ;
sld:type cwl:File .
cwl:default "output" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-O" ] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"-asn-cache" ] ;
sld:type cwl:Directory .
a cwl:CommandLineTool ;
rdfs:label "Run genomic CMsearch (Rfam rRNA), execution" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-nogenbank" ) ;
cwl:baseCommand ( "cmsearch_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 "$(inputs.asn_cache)"
]
] .
sld:type [ sld:items xsd:boolean ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "Run genomic CMsearch (Rfam rRNA), gather" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-unzip" "*" ) ;
cwl:baseCommand ( "gpx_qdump" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs .
sld:type cwl:File .
cwl:source .
cwl:default "cmsearch.asn" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"-input" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "Run genomic CMsearch (Rfam rRNA), scatter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-nogenbank" ) ;
cwl:baseCommand ( "gpx_qsubmit" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.asn_cache)"
]
] .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:default "jobs.xml" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
cwl:source .
sld:type cwl:Directory .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "Post-process CMsearch annotations" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-unique" "-nogenbank" ) ;
cwl:baseCommand ( "annot_merge" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.asn_cache)"
]
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_dir)" ] ;
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:prefix
"-asn-cache" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-model-path" ] ;
sld:type cwl:File .
cwl:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-cmsearch-path" ] ;
sld:type xsd:string , sld:null .
a cwl:Workflow ;
rdfs:label "Run genomic CMsearch (Rfam rRNA)" ;
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 .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-asn-cache" ] ;
sld:type cwl:Directory .
cwl:default "annots.asn" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-jobs" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-taxon-db" ] ;
sld:type cwl:File .