@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix Dirent: <https://w3id.org/cwl/cwl#Dirent/> .
@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/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#tax_sql_file>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#blastdb_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-blastdbs-manifest" ;
                            cwl:valueFrom              "blastdbs.mft"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#all_order_specific_blastdb>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/file2basenames.cwl>
        a                          cwl:ExpressionTool ;
        ns1:original_cwlVersion    "v1.2" ;
        ExpressionTool:expression  "${\n  var values=[];\n  var lines=[];\n  if(inputs.input != null) {\n      lines = inputs.input.contents.split(\"\\n\");\n  }\n  for(var i = 0; i<lines.length; i++) {\n    var basename = lines[i];\n    var last_slash_i = basename.lastIndexOf(\"/\");\n    if(last_slash_i>-1) {\n      basename = basename.substr(last_slash_i + 1).trim();\n    }\n    if(basename.length > 0) {\n      values.push (basename);\n    }\n  }\n  return { \"values\": values }; \n}\n" ;
        cwl:cwlVersion             cwl:v1.2 ;
        cwl:inputs                 <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/file2basenames.cwl#input> ;
        cwl:outputs                <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/file2basenames.cwl#values> ;
        cwl:requirements           [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#clust_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ouniversal-clusters" ] ;
        sld:default       "universal_clusters.inf" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#prot_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-oall" ] ;
        sld:default       "all_prots.seqid" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#all_order_specific_blastdb>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#File2Basenames>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#File2Basenames/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#File2Basenames/values> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/file2basenames.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Get Proteins, bacterial_prot_src" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-no-phage" "-nogenbank" ) ;
        cwl:baseCommand          ( "bacterial_prot_src" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#naming_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#selected_blastdb_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#clust_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#tax_sql_file> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#prot_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#all_order_specific_blastdb> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#universal_clusters> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#all_prots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#selected_blastdb> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${            var blob = '# blastdbs.mft created for bacterial_prot_src from input \"blastdb\" Array of blastdbs' +              '\\n' ;             var i = 0;            for (i = 0; i < inputs.blastdb.length; i++) {               blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i] + String.fromCharCode(10);             }             for (i = 0; i < inputs.all_order_specific_blastdb.length; i++) {               blob += inputs.blastdb_dir.path + '/' + inputs.all_order_specific_blastdb[i] + String.fromCharCode(10);             }             return blob;           }" ;
                                                  cwl:entryname  "blastdbs.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#selected_blastdb>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.selected_blastdb_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/file2basenames.cwl#input>
        cwl:inputBinding  [ cwl:loadContents  true ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/blastdb>
        cwl:linkMerge  "merge_flattened" ;
        sld:default    "blast_rules_db" , "blastdb" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/tax_sql_file>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#tax_sql_file> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#all_prots>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.prot_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/file2basenames.cwl#values>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#tax_sql_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#universal_clusters>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.clust_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app>
        rdfs:label  "Get Proteins: application run" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/tax_sql_file> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/naming_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/all_order_specific_blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/blastdb_dir> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/universal_clusters> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/all_prots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/selected_blastdb> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Get Proteins" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#File2Basenames> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#all_order_specific_blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#tax_sql_file> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#naming_sqlite> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#universal_clusters> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#all_prots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#selected_blastdb> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#naming_sqlite>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unicoll_sqlite" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#blastdb>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#all_prots>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/all_prots> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#File2Basenames/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/selected_blastdb> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#naming_sqlite>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#selected_blastdb>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#File2Basenames/values> ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/all_order_specific_blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#all_order_specific_blastdb> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#selected_blastdb_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-selected-blastdb-manifest" ] ;
        sld:default       "selected_blastdb.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/protein_alignment/bacterial_prot_src.cwl#uniColl_asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#universal_clusters>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/universal_clusters> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/naming_sqlite>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#naming_sqlite> .