@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-softmask" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-softmask" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"-ids" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-ids" ] ;
sld:type cwl:File , sld:null .
cwl:default "blastdb" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-db" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-db" ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:prefix "-asn-cache"
] ;
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:prefix "-asn-cache"
] ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"-hardmask" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-hardmask" ] ;
sld:type cwl:File , sld:null .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"-fasta" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-fasta" ] ;
sld:type cwl:File , sld:null .
cwl:default "blastdir" .
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:Workflow ;
rdfs:label "gp_makeblastdb" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ncbi/gpdev:latest"
] ;
cwl:inputs , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"-title" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-title" ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:outputEval
"$(inputs.output_db_file)" ] ;
cwl:outputBinding [ CommandOutputBinding:outputEval
"$(inputs.output_db_file)" ] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"blastdb.*" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"blastdb.*" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File , sld:null .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.found_ids_output_file)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.found_ids_output_file)" ] ;
sld:type cwl:File .
cwl:default "found_ids.mft" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-found-ids-output-manifest" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-found-ids-output-manifest" ] ;
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-dbtype" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-dbtype" ] ;
sld:type xsd:string .
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
cwl:arguments ( [ CommandLineBinding:shellQuote false ;
cwl:valueFrom "mkdir $(inputs.blastdir) && cp"
]
) ;
cwl:arguments ( [ CommandLineBinding:shellQuote false ;
cwl:valueFrom "mkdir $(inputs.blastdir) && cp"
]
) ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:source .
cwl:source .
cwl:source .
sld:type xsd:string .
sld:type cwl:File , sld:null .
cwl:in , , , , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.blastdir)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.blastdir)" ] ;
sld:type cwl:Directory .
cwl:default "found_ids.txt" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-found-ids-output" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-found-ids-output" ] ;
sld:type xsd:string .
cwl:default "blastdb.mft" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output-manifest" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output-manifest" ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"-asnt" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-asnt" ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:source .
cwl:source .
sld:type cwl:File , sld:null .
cwl:source .
a cwl:CommandLineTool ;
cwl:baseCommand ( "gp_makeblastdb" ) ;
cwl:baseCommand ( "gp_makeblastdb" ) ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ncbi/gpdev:latest"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ncbi/gpdev:latest"
] ;
cwl:inputs , , , , , , , , , , , , ;
cwl:outputs , , .
cwl:outputSource ;
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:prefix
"-asnb" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"-asnb" ] ;
sld:type cwl:File , sld:null .