@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix Dirent: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:source .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix "-A" ;
cwl:valueFrom "${if (inputs.superkingdom==2157) { return true; } else {return false; } }"
] ;
sld:type xsd:boolean .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_dir)" ] ;
sld:type cwl:Directory .
a cwl:CommandLineTool ;
rdfs:label "Run tRNAScan, 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 .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-jobs" ] ;
sld:type cwl:File .
sld:type cwl:Directory .
a cwl:Workflow ;
rdfs:label "trnascan_wnode and gpx_qdump combined" ;
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:default true ;
cwl:inputBinding [ CommandLineBinding:prefix "-B" ;
cwl:valueFrom "${if (inputs.superkingdom==2) { return true; } else {return false; } }"
] ;
sld:type xsd:boolean .
cwl:default "intermediate.asn" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
cwl:default "output" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-O" ] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
cwl:in , , , , , ;
cwl:out ;
cwl:run .
cwl:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ThirdParty/tRNAscan-SE/production/bin/tRNAscan-SE" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-tRNAscan" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"-taxid" ] ;
sld:type xsd:int .
cwl:source .
sld:type xsd:string , sld:null .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-asn-cache" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-taxon-db" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-path" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:source .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"-g" ] ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:label "Run tRNAScan, execution" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-X" "20" "-Q" "-H" "-b" "-q" "-nogenbank" ) ;
cwl:baseCommand ( "trnascan_wnode" ) ;
cwl:cwlVersion ;
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:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.asn_cache)"
]
] .