@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix cwl: .
@prefix Workflow: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.mztab_output)" ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bait).csv" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-IL_equivalent"
] ;
sld:type xsd:boolean .
sld:type cwl:File .
cwl:default "silent" ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-in"
] ;
sld:type cwl:File .
cwl:default true ;
sld:type xsd:boolean .
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/Applications/OpenMS-2.4.0/bin/PeptideIndexer" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:default "full" ;
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:source .
sld:type xsd:string .
cwl:source .
sld:type cwl:File .
a cwl:Workflow ;
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:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bait).csv" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "Rscript" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-out"
] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/Applications/OpenMS-2.4.0/bin/MztabExporter" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:default true ;
sld:type xsd:boolean .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bait).idxml" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-enzyme:specificity"
] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-out"
] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "python3" ) ;
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:outputBinding [ CommandOutputBinding:glob
"$(inputs.idxml_output)" ] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:outputSource ;
cwl:run ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-missing_decoy_action"
] ;
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:source .
cwl:in , , , , , , ;
cwl:out ;
cwl:run .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-fasta"
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-allow_unmatched"
] ;
sld:type xsd:boolean .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "python3" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-in"
] ;
sld:type cwl:File .