@prefix CommandLineBinding: .
@prefix xsd: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix Parameter: .
@prefix cwl: .
@prefix CommandLineTool: .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
Parameter:streamable true ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"coord_lines" ] ;
sld:type cwl:File .
rdfs:comment "The required columns are as follows:\n(1) target name: The name of the target sequence or profile.\n(18) from (ali coord): The start of the MEA alignment of this\n domain with respect to the sequence, numbered 1..L for a\n sequence of L residues.\n(19) to (ali coord): The end of the MEA alignment of this domain\n with respect to the sequence, numbered 1..L for a sequence of\n L residues.\n" ;
Parameter:streamable true ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"sequences" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "https://github.com/EddyRivasLab/easel" ;
rdfs:label "extract by names from an indexed sequence file" ;
ns2:original_cwlVersion "v1.0" ;
ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ;
cwl:baseCommand ( "esl-sfetch" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:stdout "sequences" .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"formatted_names_and_coords" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"formatted_names_and_coords" ] ;
sld:type cwl:File .
a cwl:Workflow ;
ns2:original_cwlVersion "v1.0" ;
ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ;
Workflow:steps , , , ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , ;
cwl:outputs , .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"per_domain_summary.txt" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "search profile(s) against a sequence database" ;
ns2:original_cwlVersion "v1.0" ;
ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ;
cwl:arguments ( "--domtblout" "per_domain_summary.txt"
[ CommandLineBinding:prefix "--cpu" ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "hmmsearch" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "hmmer" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_005305" ;
SoftwarePackage:version "3.1b2"
]
] ;
cwl:hints [ a ] ;
cwl:inputs , , ;
cwl:outputs .
cwl:format ;
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ;
ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ;
CommandLineTool:successCodes 1 , 0 ;
cwl:baseCommand ( "grep" "-v" "^#" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs ;
cwl:outputs ;
cwl:stdout "coord_lines" .
rdfs:label "sequence names to retrieve, one per line" ;
Parameter:streamable true ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:default "1.0E-5" .
a cwl:CommandLineTool ;
cwl:baseCommand ( "awk" "{print $1, $18, $19, $1}" ) ;
cwl:baseCommand ( "awk" "{print $1, $18, $19, $1}" ) ;
cwl:inputs ;
cwl:outputs ;
cwl:stdout "formatted_names_and_coords" .
rdfs:label "report sequences <= this E-value threshold in output" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-E" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "GDF format: \nspace/tabdelimited\n" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-C" ] ;
sld:type xsd:boolean .
rdfs:label "rRNA protein model to search with" ;
cwl:format ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:default true .
rdfs:label "sequence file indexed by esl-sfetch-index" ;
cwl:format , , , , ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-f"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:format ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .