@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#> .
@prefix ExpressionTool: <https://w3id.org/cwl/cwl#ExpressionTool/> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#no_internet>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#input_fasta>
        rdfs:comment      "FASTA file with user provided headers and user provided prokaryota genome" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-fasta" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/output_entries>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#input>
        rdfs:comment      "JSON file with submission and molecule specification" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter>
        cwl:in   <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/input> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/input_asn_type> ;
        cwl:out  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/output_entries> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/output_seq_submit> ;
        cwl:run  [ a                          cwl:ExpressionTool ;
                   ExpressionTool:expression  "${ if ( inputs.input_asn_type == 'seq-entry' ) { return { 'output_entries': inputs.input, 'output_seq_submit': null } } if ( inputs.input_asn_type == 'seq-submit' ) { return { 'output_entries': null, 'output_seq_submit': inputs.input } } }" ;
                   cwl:inputs                 <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/input> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/input_asn_type> ;
                   cwl:outputs                <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/output_seq_submit> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/output_entries>
                 ] .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#submol_block_json>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/input_asn_type>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Converts input JSON file to ASN.1 template" ;
        rdfs:label               "pgapx_yaml_ctl" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "pgapx_yaml_ctl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_taxid_name> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#no_internet> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_ltp_name> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#input> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#input_fasta> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#taxon_db> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_input_asn_type_name> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#ofmt> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#ignore_all_errors> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_annotation_name> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#ifmt> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_annotation> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_ltp> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#taxid> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#input_asn_type> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "asn_cleanup" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "asn_cleanup" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#outformat> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#out_annotation_name> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#inp_annotation> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#annotation> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json/output> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#submol>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/input>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/inp_annotation>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/output_annotation> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup>
        cwl:in   <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/inp_annotation> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/out_annotation_name> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/outformat> ;
        cwl:out  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/annotation> ;
        cwl:run  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#no_internet> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#taxid>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_taxid_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json/input>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#submol> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_ltp_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-ltp" ] ;
        sld:default       "genome.ltp.txt" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#ignore_all_errors>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ignore-all-errors" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type>
        cwl:in   <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type/value> ;
        cwl:run  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#input_asn_type>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_input_asn_type_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#out_annotation_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "cleaned-annotation.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#inp_annotation>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl>
        a                          cwl:ExpressionTool ;
        ns1:original_cwlVersion    "v1.2" ;
        ExpressionTool:expression  "${ return { \"value\": String(inputs.input.contents).trim() }; }\n" ;
        cwl:cwlVersion             cwl:v1.2 ;
        cwl:inputs                 <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl#input> ;
        cwl:outputs                <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl#value> ;
        cwl:requirements           [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements           [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#output_entries>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/output_entries> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2int.cwl#value>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2int.cwl#input>
        cwl:inputBinding  [ cwl:loadContents  true ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "yaml2json" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "yaml2json.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl#input> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl#output> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/outformat>
        sld:default  "text" .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:default       "JSON" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#input_asn_type>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type/value> ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2int_taxid>
        cwl:in   <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2int_taxid/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2int_taxid/value> ;
        cwl:run  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2int.cwl> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2int_taxid/input>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/taxid> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#fasta> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/input>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/annotation> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#outformat>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-outformat" ] ;
        sld:default       "text" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#ignore_all_errors>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type/input>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input_asn_type> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#no_internet>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-no-internet" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_input_asn_type_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-asn-type" ] ;
        sld:default       "input_asn_type.txt" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl#input>
        cwl:inputBinding  [ cwl:loadContents  true ] ;
        cwl:inputBinding  [ cwl:loadContents  true ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_annotation>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_annotation_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/asn_cleanup.cwl#annotation>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_annotation_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json>
        rdfs:label  "yaml2json" ;
        cwl:in      <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json/input> ;
        cwl:out     <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_ltp>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_ltp_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl>
        a                        cwl:Workflow ;
        rdfs:comment             "Prepare user input for  NCBI-PGAP pipeline" ;
        rdfs:label               "Prepare user input" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2int_taxid> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#yaml2json> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_ltp> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#fasta> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#submol> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#no_internet> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#taxon_db> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#ignore_all_errors> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#taxid> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#submol_block_json> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#locus_tag_prefix> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#input_asn_type> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#output_entries> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#output_seq_submit> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_taxid_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-taxid" ] ;
        sld:default       "taxid.txt" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl>
        rdfs:label  "pgapx_yaml_ctl" ;
        cwl:in      <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/ignore_all_errors> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta> ;
        cwl:out     <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/taxid> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input_asn_type> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/output_ltp> , <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/output_annotation> ;
        cwl:run     <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/input_asn_type>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_input_asn_type/value> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#locus_tag_prefix>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_ltp/value> ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/run/output_seq_submit>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/ignore_all_errors>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#ignore_all_errors> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#output_seq_submit>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/output_seq_submit> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#initial_cleanup/out_annotation_name>
        sld:default  "cleaned_input.asn" .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2int.cwl>
        a                          cwl:ExpressionTool ;
        ns1:original_cwlVersion    "v1.2" ;
        ExpressionTool:expression  "${ return { \"value\": parseInt(inputs.input.contents) }; }\n" ;
        cwl:cwlVersion             cwl:v1.2 ;
        cwl:inputs                 <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2int.cwl#input> ;
        cwl:outputs                <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2int.cwl#value> ;
        cwl:requirements           [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#output_annotation_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-annotation" ] ;
        sld:default       "input.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_ltp>
        cwl:in   <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_ltp/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_ltp/value> ;
        cwl:run  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/pgapx_yaml_ctl.cwl#ofmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ofmt" ] ;
        sld:default       "JSON" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2string_ltp/input>
        cwl:source  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/output_ltp> .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/file2string.cwl#value>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#taxid>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#file2int_taxid/value> ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/progs/yaml2json.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:default       "submol.json" ;
        sld:type          xsd:string .