@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix cwl: .
@prefix Workflow: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:outputBinding [ CommandOutputBinding:glob
"addOrganism.dummy" ] ;
sld:type cwl:File .
sld:type cwl:File .
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:in , , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"addblast.dummy" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"showblast.dummy" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.in_fasta.basename)"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "$(inputs.blastdb_Path)"
]
) ;
cwl:baseCommand ( "cp" ) ;
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 "$(inputs.in_fasta)"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "addfile_2_db.dummy" .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.managePy_Path)manage.py"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "addorganism" ;
cwl:valueFrom "$(inputs.scientific_name[0])"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "$(inputs.scientific_name[1])"
]
) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:stdout "addOrganism.dummy" .
sld:type xsd:string .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"addfile_2_db.dummy" ] ;
sld:type cwl:File .
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:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
sld:type xsd:string .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"makeblastdb.dummy" ] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.managePy_Path)manage.py"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "blast_utility" ;
cwl:valueFrom "$(inputs.in_fasta.basename)"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "-p"
]
) ;
cwl:baseCommand ( "python" ) ;
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 "${ var LIST = [(inputs.in_fasta)]; return LIST; }"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "populatesequence.dummy" .
sld:type cwl:File .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:source .
cwl:source .
sld:type cwl:File .
sld:type xsd:string .
cwl:in , ;
cwl:out ;
cwl:run .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type cwl:File .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"populatesequence.dummy" ] ;
sld:type cwl:File .
sld:type xsd:string .
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.managePy_Path)manage.py"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "addblast" ;
cwl:valueFrom "$(inputs.scientific_name[0])"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "$(inputs.scientific_name[1])"
]
[ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-t" ;
cwl:valueFrom "nucleotide"
]
[ CommandLineBinding:position 4 ;
cwl:valueFrom "Genome"
]
[ CommandLineBinding:position 5 ;
cwl:valueFrom "Assembly"
]
[ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-f" ;
cwl:valueFrom "$(inputs.in_fasta.basename)"
]
[ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-d" ;
cwl:valueFrom "$(inputs.scientific_name[0]) $(inputs.scientific_name[1]) genome assembly, $(inputs.tree[1])"
]
) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${ var LIST = [(inputs.in_fasta)]; return LIST; }"
] ;
cwl:stdout "addblast.dummy" .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.managePy_Path)manage.py"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "blast_utility" ;
cwl:valueFrom "$(inputs.in_fasta.basename)"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "-m"
]
) ;
cwl:baseCommand ( "python" ) ;
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 "${ var LIST = [(inputs.in_fasta)]; return LIST; }"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "makeblastdb.dummy" .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(inputs.managePy_Path)manage.py"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "blast_shown" ;
cwl:valueFrom "$(inputs.in_fasta.basename)"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--shown" ;
cwl:valueFrom "true"
]
) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${ var LIST = [(inputs.in_fasta)]; return LIST; }"
] ;
cwl:stdout "showblast.dummy" .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type xsd:string .