@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/fasta_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#fasta_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/id_deleted_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "id_deleted_file.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "id_deleted_file.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/id_deleted_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/id_deleted_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/gap_lines>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "lines-contain-N.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "lines-contain-N.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/id_deleted_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/gap_lines> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-ne" ;
                                         cwl:valueFrom                "print if /N/"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.id_deleted_file.basename)"
                                       ]
                                     ) ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-ne" ;
                                         cwl:valueFrom                "print if /N/"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.id_deleted_file.basename)"
                                       ]
                                     ) ;
                   cwl:baseCommand   ( "perl" ) ;
                   cwl:baseCommand   ( "perl" ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/id_deleted_file> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/gap_lines> ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.id_deleted_file)]; return LIST; }"
                                     ] ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.id_deleted_file)]; return LIST; }"
                                     ] ;
                   cwl:stdout        "lines-contain-N.txt"
                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/fasta_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#fasta_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gap_lines>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/gap_lines> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#fasta_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gap_lines> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/fasta_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/id_deleted_file> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-v" ;
                                         cwl:valueFrom                ">"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.fasta_file.basename)"
                                       ]
                                     ) ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-v" ;
                                         cwl:valueFrom                ">"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.fasta_file.basename)"
                                       ]
                                     ) ;
                   cwl:baseCommand   ( "grep" ) ;
                   cwl:baseCommand   ( "grep" ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/fasta_file> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/id_deleted_file> ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.fasta_file)]; return LIST; }"
                                     ] ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.fasta_file)]; return LIST; }"
                                     ] ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:stdout        "id_deleted_file.txt"
                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/id_deleted_file>
        sld:type  cwl:File .