@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 ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@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/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences>
        rdfs:label  "Assign SPARCL Architecture Names to Proteins" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/lds2> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#nuc_fasta>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.nuc_fasta_name)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/sure_cutoff>
        sld:default  1.5e-01 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#compart>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-compart" ] ;
        sld:type          xsd:boolean , sld:null .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#xml_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "protein_assignments.xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#fasta_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#precedence_filename>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-precedences" ] ;
        sld:default       "precedences.tsv" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#max_unannotated_region>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-unannotated-region" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blast_align> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#onon_match_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-non-match-output" ] ;
        sld:default       "align-nomatch.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#proteins_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-proteins" ] ;
        sld:default       "proteins.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta>
        rdfs:label  "Assign SPARCL Architecture Names to Proteins" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/serial> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/i> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/prots_only> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/fasta_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/type> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/fasta> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-workers" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/threshold>
        sld:default  20 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#files_in>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hits-output" ] ;
        sld:default       "retrieved_hits.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#naming_sqlite>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.hits_output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#defline_cleanup_rules>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#comp_based_stats>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-comp_based_stats" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/long_model_limit>
        sld:default  1000000 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#extra_coverage>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#max_batch_length>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-batch-length" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/dbsize>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#dbsize> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/fasta_name>
        sld:default  "proteins.fa" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#output_xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "asn2fasta" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "asn2fasta" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#i> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#serial> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#prot_fasta_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#feats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#nuc_fasta_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#fasta_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#prots_only> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#nuc_fasta> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#prot_fasta> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#fasta> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "bact_annot_filter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "bact_annot_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#long_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#input_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#out_annotation_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#thr> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#max_unannotated_region> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#abs_short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#max_overlap> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#short_model_limit> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#out_annotation> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# annotation.mft created for bact_annot_filter.mft from input input Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "annotation.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.not_found_output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/allow_intersection>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#allow_intersection> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/prot_ids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blastdb>
        rdfs:label  "Input blastdb databases" ;
        sld:type    [ sld:items  xsd:string ;
                      sld:type   sld:array
                    ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#top>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-top" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#fasta>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.fasta_name)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/extra_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#extra_coverage> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#b>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#allow_intersection>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/ofmt>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#ofmt> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#input_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#affinity>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-affinity" ] ;
        sld:default       "subject" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#delay>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-delay" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#suffix>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--additional-suffix=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:default       ".xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#s>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#out_annotation>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_annotation_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/sqlite_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/orfs> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/not_found_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/hits_output> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/k>
        sld:default  "query,subject,-score,-num_ident,query_align_len,subject_align_len,query_start,subject_start" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/batch_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#batch-size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#short_protein_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-short-protein-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#seg>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-seg" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#chunk_size>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-l"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#protein_assignments>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.xml_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gp_fetch_sequences" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "gp_fetch_sequences" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#out_asn_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#output> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#genus_list>
        sld:type  [ sld:items  xsd:int ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "add_prot_names_to_annot" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "add_prot_names_to_annot" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#submission_mode_genbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#out_annotation_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#proteins_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#defline_cleanup_rules> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#proteins> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#out_annotation> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# proteins.mft created for add_prot_names_to_annot from input proteins Array of Files\\n'; for (var i = 0; i < inputs.proteins.length; i++) { blob += inputs.proteins[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "proteins.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#identification_db_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "prepare_sparclbl_input" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "prepare_sparclbl_input" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#other_assignments_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#other_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#precedence_filename> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#prot_ids_filename> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#precedences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#prot_ids> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# other_assignments.mft created for prepare_sparclbl_input from input other_assignments Array of Files\\n'; for (var i = 0; i < inputs.other_assignments.length; i++) { blob += inputs.other_assignments[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "other_assignments.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/allow_intersection>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subseq_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subseq-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_xml_jobs)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/top_by_score>
        sld:default  10 .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#word_size>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/ifmt>
        sld:default  "seq-align-set" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-b" ;
                            cwl:valueFrom              "$(inputs.b.path)/$(inputs.blastdb)"
                          ] ;
        sld:default       "cdd" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#n>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-n" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/input_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/unzip> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#dbsize>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-dbsize" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "align_filter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "align_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#subject_allowlist> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#query_allowlist_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#compartments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#o_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#input_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#subject_allowlist_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#onon_match_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#ifmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#compartments_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#query_allowlist> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#onon_match> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#o> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# query_allowlist.mft created for align_filter from input \"query_allowlist\" File\\n'; if ( inputs.query_allowlist  == null) { return blob; } else { blob += inputs.query_allowlist.path + '\\n';  return blob; }}" ;
                                                  cwl:entryname  "query_allowlist.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# aligns.mft created for align_filter from input \"input\" Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "aligns.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${\n  var blob = '# compartments.mft created for align_filter from input \"compartments\" Array of Files\\n';\n  if (inputs.compartments) {  \n    for (var i = 0; i < inputs.compartments.length; i++) {\n      blob += inputs.compartments[i].path + '\\n';\n    }\n  }\n  return blob;\n}\n" ;
                                                  cwl:entryname  "compartments.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# subject_allowlist.mft created for align_filter from input \"subject_allowlist\" File\\n'; if ( inputs.subject_allowlist == null) { return blob; } else { blob += inputs.subject_allowlist.path + '\\n';  return blob; }}" ;
                                                  cwl:entryname  "subject_allowlist.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/comp_based_stats>
        sld:default  "F" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins>
        rdfs:label  "Assign Clusters to Proteins: actual task" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/cutoff> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/namedb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/hfmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/sure_cutoff> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/namedb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/task> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/margin> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/protein_assignments> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#out_asn_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "out_asn_name.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blast_type>
        sld:default  "predicted-protein" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/comp_based_stats>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#comp_based_stats> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/compart>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/unicoll_sqlite>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#naming_sqlite> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Good_AntiFam_filtered_proteins_gilist>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Extract_Model_Proteins_prot_ids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#evalue>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#genus_list>
        sld:type  [ sld:items  xsd:int ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#query_allowlist>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Extract_Model_Proteins_prot_ids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "sparclbl" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "sparclbl_mp.sh" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#b> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#d> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#n> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#p> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#protein_assignments_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#s> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#m> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#protein_assignments> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  15000
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/margin>
        sld:default  5e-02 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#abs_short_model_limit>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-abs-short-model-limit" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/no_merge>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#no_merge> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#compartments_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-compartments-manifest" ] ;
        sld:default       "compartments.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#compartments>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#seg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/top_by_score>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#top_by_score> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/namedb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#identification_db_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#annotation>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/threshold>
        sld:default  21 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/limit_mem>
        sld:default  "13G" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#overlap>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-overlap" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#batch_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-batch-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/max_overlap>
        sld:default  120 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#feats>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-feats" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#i>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#word_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-word_size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/files_in>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blast_align> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/protein_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#hmm_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#wp_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/protein_assignments> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Good_AntiFam_filtered_proteins_gilist> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/align_filter>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#align_filter> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/ofmt>
        sld:default  "asn-binary" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/input>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/out_annotation> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#d>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-d" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/hfmt>
        sld:default  "seq-align" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_hits_cache>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_jobs> .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#queries_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-queries-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_target_seqs>
        sld:type  xsd:int .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#hits>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hits" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/seg>
        sld:default  "no" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#extra_coverage>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#filter>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-filter" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#cutoff>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-cutoff" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#no_merge>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/ifmt>
        sld:default  "seq-align-set" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#submission_mode_genbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-submission-mode-genbank" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_asn_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/seg>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#seg> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/dbsize>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#dbsize> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#scatter_gather_nchunks>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/workers_per_cpu> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/proteins> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-orfs-manifest" ] ;
        sld:default       "ids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/not_found_output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/seg>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#seg> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#comp_based_stats>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.mask)?*$(inputs.suffix)" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/word_size>
        sld:default  5 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#out_annotation>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/out_annotation> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/short_model_limit>
        sld:default  180 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#p>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-p" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#sure_cutoff>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-sure-cutoff" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/short_protein_threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#short_protein_threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#align_filter>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/file_out> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/hits_output> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#namedb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#dbsize>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blast_hits_cache>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_jobs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/max_unannotated_region>
        sld:default  5000 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "output.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#scatter_gather_nchunks>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#NxM_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-NxM-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#input_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "aligns.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#CDDdata2>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/orfs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers_per_cpu>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-workers-per-cpu" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_target_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_target_seqs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl>
        rdfs:label  "Assign SPARCL Architecture Names to Proteins" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/d> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/m> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/n> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/p> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/s> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/b> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/protein_assignments> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "cwl split wrapper" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "split" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#mask> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#suffix> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#chunk_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#nchunks> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#extra_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-extra-coverage" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/affinity>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#affinity> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-not-found-output" ] ;
        sld:default       "not_found.ids" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#genus_list>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-genus-list"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  xsd:int ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/unicoll_sqlite>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#naming_sqlite> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#evalue>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits>
        rdfs:label  "Find best protein hits" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/ifmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/nogenbank> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/o> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#allow_intersection>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#thresholds>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#input_jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/abs_short_model_limit>
        sld:default  60 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "cluster_blastp_wnode and gpx_qdump combined" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#dbsize> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blast_align> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/soft_masking>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#soft_masking> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#top_by_score>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ofmt>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#serial>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-serial" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#short_model_limit>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-short-model-limit" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blastdb>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blast_rules_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blastdb> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/unicoll_sqlite>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#naming_sqlite> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/workers_per_cpu>
        sld:default  1e+00 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#nchunks>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-n l//" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#o_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/submission_mode_genbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/no_merge>
        sld:default  false .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter>
        rdfs:label  "Bacterial Annot Filter" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/abs_short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/max_unannotated_region> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/long_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/nogebank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/thr> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/max_overlap> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/asn_cache> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/out_annotation> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#long_model_limit>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-long-model-limit" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "align_sort" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "align_sort" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#group> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#output_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#ifmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#input_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#top> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#k> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#input> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blast_rules_db>
        rdfs:label   "parameter to store the literal 'blast_rules_db'" ;
        sld:default  "blast_rules_db" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/scatter_gather_nchunks>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#scatter_gather_nchunks> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/namedb>
        sld:default  "blast_rules_db" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#CDDdata>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#align_filter>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/nogebank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/b>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#CDDdata> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#onon_match>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.onon_match_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#no_merge>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#unzip>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/s>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/fasta> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort>
        rdfs:label  "Assign Clusters to Proteins: pre-sort alignments" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/limit_mem> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/k> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/ifmt> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/max_jobs>
        sld:default  1 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "This workflow is specialized for the case when there is an LDS2 input  LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n  proteins:\n    default:\n        class: File\n        path: '/dev/null'\n        basename: 'null'\n        contents: ''\n" ;
        rdfs:label               "gpx_qsubmit" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#queries_gc_id_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#output_xml_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#xml_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#NxM_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subseq_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#batch_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#overlap> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subjects_gc_id_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#jobs> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path  + '\\n';}return blob;}" ;
                                                  cwl:entryname  "ids.mft"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ]
                                 ] .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#soft_masking>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#annotation> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/evalue>
        sld:default  1e-01 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#threshold>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/word_size>
        sld:default  6 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#file_out>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "cat.out" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#out_annotation_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "annotation.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#out_annotation>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_annotation_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/compart>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#compart> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#precedences>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.precedence_filename)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/n>
        sld:default  500 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_jobs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/align_filter>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#align_filter> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#m>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-m" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#dbsize>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#no_merge>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-no-merge" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/unzip>
        sld:default  "*" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins>
        rdfs:label  "Add Names to Proteins" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/defline_cleanup_rules> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/submission_mode_genbank> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/out_annotation> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "cluster_blastp_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "cluster_blastp_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#delay> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers_per_cpu> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#backlog> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#evalue> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#outdir> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  true ;
                                                  cwl:entry        "$(inputs.lds2)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  5000
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#namedb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-namedb" ;
                            cwl:valueFrom              "$(inputs.namedb_dir.path)/$(inputs.namedb)"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#query_allowlist_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-query-allowlist" ] ;
        sld:default       "query_allowlist.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#defline_cleanup_rules>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-defline-cleanup-rules" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#compart>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/other_assignments>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/protein_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#hmm_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#wp_assignments> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#proteins>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/defline_cleanup_rules>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#defline_cleanup_rules> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_target_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_target_seqs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#naming_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#hmm_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#identification_db_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blast_rules_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#defline_cleanup_rules> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#CDDdata> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#wp_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Extract_Model_Proteins_prot_ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#CDDdata2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Good_AntiFam_filtered_proteins_gilist> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#thresholds> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#annotation> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#out_annotation> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#input_jobs>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/comp_based_stats>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#comp_based_stats> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/max_batch_length>
        sld:default  10000 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#wp_assignments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/files_in> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/file_out> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#backlog>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-backlog" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/blast_type>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_type> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#mask>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            cwl:valueFrom                "$(inputs.mask)"
                          ] ;
        sld:default       "jobs" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/cutoff>
        sld:default  5e-01 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/type>
        sld:default  "seq-entry" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-jobs" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/max_target_seqs>
        sld:default  50 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gpx_qdump" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-produce-empty-file" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#input_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#unzip> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#seg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#ofmt>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#blast_type>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-blast-type" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#hfmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hfmt" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#soft_masking>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/d>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#CDDdata2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ids>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/no_merge>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#no_merge> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gp_fetch_sequences.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#o>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.o_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input>
        rdfs:label  "Prepare SPARCLBL input" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/other_assignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/unicoll_sqlite> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/precedences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/prot_ids> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#seg>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-seg" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#type>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-type" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#identification_db_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#top_by_score>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-top-by-score" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#prot_fasta_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-op" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#affinity>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/evalue>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#evalue> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#prot_ids_filename>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "prot.seq_ids" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#k>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-k" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/o> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#comp_based_stats>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-comp_based_stats" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#prots_only>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-prots-only" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#task>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-task" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "orf_hits_cache_retrieve" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "orf_hits_cache_retrieve" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#sqlite_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${\n  var blob = '# ids.mft created for orf_hits_cache_retrieve from input \"orfs\" Array of Files' +\n    String.fromCharCode(10) ; \n  for (var i = 0; i < inputs.orfs.length; i++) { \n    blob += inputs.orfs[i].path + String.fromCharCode(10); \n  } \n  return blob; \n}" ;
                                                  cwl:entryname  "ids.mft"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#max_overlap>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-overlap" ] ;
        sld:type          xsd:int , sld:null .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#align_filter>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-align_filter" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Add_Names_to_Proteins/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_target_seqs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_target_seqs" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/task>
        sld:default  "blastp" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#top_by_score>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#ofmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ofmt" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/i>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences/output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/nchunks>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#scatter_gather_nchunks> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/p>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Prepare_SPARCLBL_input/precedences> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/compart>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#compart> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/soft_masking>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#soft_masking> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#input>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#thr>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-thr" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#out_annotation_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "out-annotation.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/align_filter>
        sld:default  "score>0 && pct_identity_gapopen_only > 35" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#prot_ids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.prot_ids_filename)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids-manifest" ] ;
        sld:default       "ids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank> .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "assign_cluster" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "assign_cluster" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#task> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#margin> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#xml_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#hfmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#namedb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#cutoff> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#sure_cutoff> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#namedb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#lds2> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#protein_assignments> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.namedb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/prots_only>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/word_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#word_size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/genus_list>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#genus_list> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#evalue>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-evalue" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/allow_intersection>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#allow_intersection> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subjects_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subjects-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump>
        cwl:in       <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/threshold> ;
        cwl:out      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blast_align> ;
        cwl:run      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/input_jobs> ) .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/seg>
        sld:default  "30 2.2 2.5" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#hmm_assignments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#other_assignments_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-other-assignments" ] ;
        sld:default       "other_assignments.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#comp_based_stats>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#protein_assignments>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.protein_assignments_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta/serial>
        sld:default  "binary" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/ofmt>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ofmt> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/outdir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/filter>
        sld:default  "subject_coverage >= 10" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#prot_fasta>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.prot_fasta_name)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#subject_allowlist_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subject-allowlist" ] ;
        sld:default       "subject_allowlist.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "blastp_wnode_naming" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#batch-size> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_align> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#compart>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#input>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#word_size>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#threshold>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/sparclbl.cwl#protein_assignments_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "proteins.xml" ;
        sld:type          xsd:string , sld:null .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/affinity>
        sld:default  "subject" .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits>
        rdfs:label  "Find Naming Protein Hits" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/delay> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/allow_intersection> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blast_align> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_best_protein_hits/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#allow_intersection>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-allow-intersection" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#short_protein_threshold>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bact_annot_filter.cwl#input_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "annotation.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/asn2fasta.cwl#nuc_fasta_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-on" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/add_prot_names_to_annot.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#margin>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-margin" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/hits>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/dbsize>
        sld:default  "6000000000" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/batch_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/ids> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#soft_masking>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-soft_masking" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_target_seqs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#uniColl_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_batch_length>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_sort.cwl#group>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-group" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/comp_based_stats>
        sld:default  "F" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/genus_list>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#genus_list> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/word_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#word_size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/assign_cluster.cwl#threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/soft_masking>
        sld:default  "yes" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#sqlite_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-blast-hits-sqlite-cache" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/evalue>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#evalue> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/delay>
        sld:default  0 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/top_by_score>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#top_by_score> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_type>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "file concatenation" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "cat" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#files_in> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#file_out> ;
        cwl:stdout               "cat.out" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/thr>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#thresholds> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#batch-size>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins_sort/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/prepare_sparclbl_input.cwl#other_assignments>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Find_Naming_Protein_Hits/blast_hits_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#blast_hits_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/align_filter.cwl#subject_allowlist>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/extra_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#extra_coverage> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl/m>
        sld:default  20 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/sqlite_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_hits_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#Assign_Clusters_to_Proteins/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl#sequence_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/max_batch_length>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_batch_length> .