@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/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/link_to_publication>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#link_to_publication> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/create_readme.cwl#readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/url> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/url> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme>
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme/readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/create_readme.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nThe file $(inputs.original_gff.basename) was post-processed to add functional annotations from the AgBase functional annotation pipeline (https://github.com/agbase). The resulting file is: $(inputs.processed_gff.basename). This file was used for all operations within the i5k Workspace.' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#processed_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#readme_file> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#original_gff> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/url> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#original_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#organization> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_protein_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#processed_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#path_GO> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_cds_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_transcript_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#link_to_publication> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_genomic_gff> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/url>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#organization>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme/readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/original_gff>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#original_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/readme_file> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/url> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#readme_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme/readme_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nInformation about this dataset can be found here: \nInformation about the publication of this dataset can be found here: $(inputs.link_to_publication)' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#readme_file> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#link_to_publication> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#tree> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#out_readme_file> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/url>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#processed_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/url>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_transcript_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl#organization>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#processed_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/link_to_publication> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_protein_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#path_GO>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2>
        cwl:in    <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/original_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/processed_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/readme_file> ;
        cwl:out   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/out_readme_file> ;
        cwl:run   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl> ;
        cwl:when  "$(inputs.path_GO != null)" .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl#readme_file> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl#url> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeInfo-genePred.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_cds_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/organization>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#organization> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo 'The following files were retrieved from $(inputs.organization) on ${var A = new Date(); var year = A.getFullYear(); var month = A.getMonth()+1; var day = A.getDate(); var date = year + '-' + day + '-' + month;  return date;}:' > readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl#readme_file> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl#organization> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/organization> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl#url>
        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
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeURL.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred_annotation.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeFirstLine.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1>
        cwl:in    <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1/readme_file> ;
        cwl:out   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1/out_readme_file> ;
        cwl:run   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred.cwl> ;
        cwl:when  "$(inputs.path_GO == null)" .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nThe file was post-processed to [describe post-processing, if any]. The resulting file is: [Filename]. This file was used for the JBrowse genome browser and the Apollo manual curation tool.' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred.cwl#readme_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/writeLastLine-genePred.cwl#out_readme_file> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/create_readme.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "touch" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/create_readme.cwl#readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/out_readme_file> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/url>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_create_readme/readme-genePrediction-workflow.cwl#url_cds_fasta> .