@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix cwl: .
@prefix Workflow: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:source .
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:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-host" ;
cwl:valueFrom "$(inputs.host[0])"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-organism" ;
cwl:valueFrom "$(inputs.scientific_name[0])_$(inputs.scientific_name[1])"
]
[ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-genus" ;
cwl:valueFrom "$(inputs.scientific_name[0])"
]
[ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-species" ;
cwl:valueFrom "$(inputs.scientific_name[1])"
]
[ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "-directory" ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_apollo2_data[0])"
]
[ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "-blatdb" ;
cwl:valueFrom "$(inputs.PATH[2])/$(inputs.tree[0])/$(inputs.genome_fasta_name[0]).2bi"
]
[ CommandLineBinding:position 13 ;
CommandLineBinding:prefix "-username" ;
cwl:valueFrom "$(inputs.login_apollo2[0])"
]
[ CommandLineBinding:position 15 ;
CommandLineBinding:prefix "-password" ;
cwl:valueFrom "$(inputs.login_apollo2[1])"
]
[ CommandLineBinding:position 17 ;
cwl:valueFrom "-publicMode"
]
) ;
cwl:baseCommand ( "createOrganism.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"shallow_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "createOrganism.log" .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:in ;
cwl:run .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"createOrganism.log" ] ;
sld:type cwl:File .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.in_createOrganismLog)"
]
) ;
cwl:baseCommand ( "cat" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${ var LIST = [(inputs.in_createOrganismLog)]; return LIST; }"
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:in , , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .