@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix cwl: .
@prefix Workflow: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:outputBinding [ CommandOutputBinding:glob
"analyses_symlink.dummy" ] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:source .
cwl:source .
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 "-s" ;
cwl:valueFrom "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/Current\\ Genome\\ Assembly"
]
) ;
cwl:baseCommand ( "ln" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-s" ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gaps.bigwig.gz"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/5.Other files/Gaps in Assembly/."
]
) ;
cwl:baseCommand ( "ln" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "bigwig_symlink-gaps.dummy" .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , , , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:in , , , ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-9" ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.genome_fasta_name[0])"
]
) ;
cwl:baseCommand ( "gzip" ) ;
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:stdout "scaffold_gzip.dummy" .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"setup_folder.dummy" ] ;
sld:type cwl:File .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"bigwig_symlink-gc.dummy" ] ;
sld:type cwl:File .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-s" ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gc.bigwig.gz"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/5.Other files/GC Content/."
]
) ;
cwl:baseCommand ( "ln" ) ;
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:stdout "bigwig_symlink-gc.dummy" .
cwl:source .
sld:type cwl:File .
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 [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:in , , , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
sld:type xsd:string .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"analysis_symlink_protein.dummy" ] ;
sld:type cwl:File .
sld:type xsd:string .
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
] .
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 "-s" ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.transcript_fasta_name[0])"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.cds_fasta_name[0])"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.gff_name[0])"
]
[ CommandLineBinding:position 4 ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/readme.txt"
]
[ CommandLineBinding:position 5 ;
cwl:valueFrom "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/2.Official or Primary Gene Set/$(inputs.tree[2])/."
]
) ;
cwl:baseCommand ( "ln" ) ;
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:stdout "analyses_symlink.dummy" .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"bigwig_gzip.dummy" ] ;
sld:type cwl:File .
sld:type xsd:string .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"bigwig_symlink-gaps.dummy" ] ;
sld:type cwl:File .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
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
] .
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
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File .
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:source .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type xsd:string .
sld:type cwl:File .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"scaffold_symlink.dummy" ] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-s" ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.genome_fasta_name[0]).gz"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/readme.txt"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/1.Genome Assembly/$(inputs.tree[1])/Scaffolds/."
]
) ;
cwl:baseCommand ( "ln" ) ;
cwl:cwlVersion