@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 rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_cds_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(decodeURIComponent(inputs.in_data.location.slice(7)))"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.in_data.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" "-r" "-T" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#deepPATH_1> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                cwl:LoadListingRequirement ;
                                   cwl:loadListing  "no_listing"
                                 ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_extract>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_protein_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_gc_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_gc_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_1> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_md5checksums> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_tracks_conf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_2bi>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_md5checksums>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_apollo2_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-si" ;
                                     cwl:valueFrom                "../../scaffold/bigwig"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "-t" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse/data"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl#in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl#tree> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_protein_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_genePrediction_readme>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genePrediction_readme> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#deepPATH>
        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
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_assembly_readme>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_assembly_readme> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_seq>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_seq> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_seq>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_names>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#in_data>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "$(inputs.in_data.location.slice(7))"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "$(inputs.in_data.location.slice(7))"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "$(inputs.in_data.location.slice(7))"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#PATH> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_gc_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_tracks> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_trackList_json_bak>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_trackList_json_bak> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_trackList_json>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_trackList_json> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#gap_lines> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_trackList_json> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_tracks_conf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#in_2bi> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_protein_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_gaps_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_gc_bigwig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_apollo2_data>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_genePrediction_readme> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_transcript_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_tracks> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_genePrediction_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/gap_lines> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_gc_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_trackList_json> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_cds_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_analyses> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_gaps_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_tracks_conf> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_protein_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_functional_annotation> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/processed_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_seq> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_assembly_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_names> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/original_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_trackList_json_bak> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/original_gff>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#original_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_1> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files>
        cwl:in    <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_check> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_extract> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_md5checksums> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/url_string> ;
        cwl:run   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl> ;
        cwl:when  "$(inputs.url_string != \"NA NA NA NA NA\\n\" )" .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff>
        cwl:in    <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_1> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/processed_gff> ;
        cwl:run   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl> ;
        cwl:when  "$(inputs.processed_gff != null)" .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_functional_annotation>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_genomic_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl#tree>
        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_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_trackList_json_bak> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_assembly_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#out_dummy>
        cwl:outputSource  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_extract>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_extract> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_md5checksums>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_md5checksums> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#processed_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_trackList_json_bak> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_seq> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_genePrediction_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#gap_lines> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_tracks_conf> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_gc_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_assembly_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_names> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_tracks> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_gaps_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#original_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_functional_annotation> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#in_2bi>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_trackList_json_bak>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#url_string> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/in_2bi> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#tree>
        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
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation>
        cwl:in    <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/deepPATH_1> ;
        cwl:run   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl> ;
        cwl:when  "$(inputs.in_data !== null && inputs.tree.length > 3 && inputs.tree[3] !== \"NA\")" .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/in_2bi>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_2bi> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#tree>
        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_dispatch/2other_species/workflow.cwl#cp_names/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_names> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_gaps_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_gaps_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_functional_annotation>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_functional_annotation> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_tracks>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#deepPATH_1>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-si" ;
                                     cwl:valueFrom                "../../scaffold/analyses"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "-t" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse/data"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl#in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl#tree> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_check>
        sld:type  cwl:File .

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

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "setup_folder.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_cds_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_check>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_tracks>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_transcript_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_extract> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#tree> .

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

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_check> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/deepPATH_analyses> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_1> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#processed_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_protein_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#tree>
        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
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_names>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_gc_bigwig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_extract>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_functional_annotation> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#gap_lines> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_2bi> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_functional_annotation> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_names> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genomic_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_gc_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_assembly_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_extract> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_tracks_conf> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#original_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_gaps_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_seq> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_md5checksums> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#url_string> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genePrediction_readme> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#processed_gff> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_check> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_tracks> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_trackList_json_bak> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#original_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_gaps_bigwig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#url_string>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl#PATH>
        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_dispatch/2blat/workflow.cwl#cp_2bi/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#in_2bi> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_transcript_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig/in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genePrediction_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#deepPATH> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir_4_annotation.cwl#deepPATH_2>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#deepPATH>
        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_dispatch/workflow.cwl#2other_species/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#gap_lines> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_assembly_readme> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl#PATH>
        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
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

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

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/deepPATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_cds_fasta>
        sld:type  cwl:File .

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

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2blat/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_gaps_bigwig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_cds_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#PATH>
        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_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_dir.cwl#in_data>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_1>
        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
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_trackList_json_bak>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2working_files/in_check>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_check> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[2])/$(inputs.tree[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl#in_data> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_transcript_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses/in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_1> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl#in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl#PATH> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_bigwig.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_md5checksums>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_check> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_dummy> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_check> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_extract> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#in_md5checksums> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#tree> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_extract/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_tracks_conf>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_tracks_conf> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_names>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_names> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/deepPATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_analyses/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_functional_annotation/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_seq>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genomic_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#PATH>
        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
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_1> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#link_bigwig/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "creating directory tree" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-p" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse/data"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/bigwig"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/remap"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     cwl:valueFrom                "$(inputs.PATH[2])/$(inputs.tree[0])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "mkdir" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#PATH> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/setup_folder.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "setup_folder.dummy" .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_2> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_1> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#2other_species/in_tracks>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_tracks> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/workflow.cwl#cp_2bi/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2blat/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig>
        cwl:in    <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/in_data> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/gap_lines> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/deepPATH> ;
        cwl:run   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file.cwl> ;
        cwl:when  "$(inputs.gap_lines.size > 0)" .

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

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#gap_lines>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_2>
        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
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums>
        cwl:in   <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/PATH> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/tree> , <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/cp_file.cwl> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_genePrediction_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_genomic_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2working_files/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_names/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_transcript_fasta> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_seq/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_seq> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/2other_species/workflow.cwl#in_tracks_conf> .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#gap_lines>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_assembly_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/workflow.cwl#in_functional_annotation>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/1349cd892472557835cbeb736b9e9c7e8b289fa0/flow_dispatch/link_analyses.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .