@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix Dirent: <https://w3id.org/cwl/cwl#Dirent/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .
@prefix ExpressionTool: <https://w3id.org/cwl/cwl#ExpressionTool/> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#db_gencode>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_impl)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_dump/seed_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#seqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#superkingdom>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-superkingdom" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#sorted_seeds>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#align_non_match>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/align_non_match> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#max_extent>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_extent" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/gc_assembly>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#gc_assembly> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#limit_mem>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-limit-mem" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter Protein Seeds, compart" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-compartment_penalty" "0.10" "-max_extent" "100" "-max_intron" "100" "-maximize" "coverage" "-min_compartment_idty" "0.05" "-min_singleton_idty" "0.05" "-nogenbank" "-prosplign-gaps" "-ifmt" "seq-align" ) ;
        cwl:baseCommand          ( "prosplign_compart" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#seed_hits> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#unfilt_comp> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  15000
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#tax_sql_file> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#min_scaffold_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-min_scaffold_coverage" ] ;
        sld:default       5e-01 ;
        sld:type          xsd:float .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/db_gencode>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#db_gencode> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#prosplign>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#compartments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/prosplign>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/prosplign_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat/file_in_1st>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#filter_accept>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-filter-accept" ] ;
        sld:default       "pct_coverage = 100 AND qframe = 0 AND sframe = 0 AND cds_internal_stops = 0" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qdump>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qdump/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qdump/prosplign_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat/file_in_2nd>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#prosplign> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Search Compartments, execute\"" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-comp_based_stats" "F" "-dbsize" "6000000000" "-delay" "0" "-evalue" "0.1" "-gapextend" "2" "-gapopen" "9" "-matrix" "BLOSUM62" "-seg" "no" "-soft_masking" "true" "-threshold" "12" "-word_size" "3" "-nogenbank" ) ;
        cwl:baseCommand          ( "tblastn_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#outdir> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  3000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/db_gencode>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int/value> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "blast.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#prosplign_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qdump/prosplign_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compartments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat/file_in_2nd> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat/file_in_1st> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat/file_out> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/seed_hits>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/blast_partial_cov> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl#file_in_2nd>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#gc_assembly>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Search Compartments, execute\"" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-compartment_penalty" "0.10" "-cut_flank_partial_codons" "true" "-cut_flanks_with_posit_drop" "true" "-cut_flanks_with_posit_dropoff" "40" "-cut_flanks_with_posit_gap_ratio" "18" "-cut_flanks_with_posit_max_len" "48" "-cut_flanks_with_posit_window" "150" "-fill_holes" "true" "-flank_positives" "49" "-frameshift_opening" "30" "-gap_extension" "1" "-gap_opening" "10" "-intron_AT" "25" "-intron_GC" "20" "-intron_GT" "15" "-intron_non_consensus" "34" "-inverted_intron_extension" "1000" "-max_bad_len" "45" "-max_extent" "100" "-max_intron" "100" "-max_overlap" "60" "-maximize" "coverage" "-min-jobs" "5" "-min_compartment_idty" "0.05" "-min_exon_ident" "30" "-min_exon_positives" "55" "-min_flanking_exon_len" "41" "-min_good_len" "41" "-min_intron_len" "30" "-min_positives" "15" "-min_singleton_idty" "0.05" "-score_matrix" "BLOSUM62" "-start_bonus" "8" "-stop_bonus" "8" "-total_positives" "55" "-allow_alt_starts" "-no_introns" "-nogenbank" ) ;
        cwl:baseCommand          ( "prosplign_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#outdir> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  4000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Filter Protein Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#blast_full> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#prosplign> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_non_match> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#db_gencode>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-db_gencode" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/compartments>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#asn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Protein Alignments, gather" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-unzip" "*" "-num-partitions" "1" ) ;
        cwl:baseCommand          ( "gpx_make_outputs" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#input_path> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/unfilt_comp>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/unfilt_comp> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/asn>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Filter Protein Seeds; Find ProSplign Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qdump> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#gc_assembly> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#seed_hits> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#prosplign_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#compartments>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl#prosplign_align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#seed_hits>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "blast.#.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter Protein Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-filter" "pct_identity_gapopen_only >= 50 AND NOT (pct_coverage < 20 and (query_entropy < 0.3 OR query_seg_pct > 60)) AND ( (query_start<=20 AND SUB(query_length, query_end)<=20) OR pct_identity_gapopen_only >= 60 ) AND (SUB(subject_end, subject_start) > 90 || SUB(subject_end, subject_start) > MUL(query_length,1.5) || num_ident >=60) AND (query_length > 30 || (pct_identity_gap >= 80 AND SUB(subject_end, subject_start) >= MUL(query_length,2.4)))" "-ifmt" "seq-align" "-nogenbank" ) ;
        cwl:baseCommand          ( "align_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output_non_match> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#file_in> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align_non_match> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align_non_match>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_non_match)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_dump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/outdir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#sufficient_compart_length>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-sufficient_compart_length" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/gencode>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/blastdb_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Seed Protein Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/gc_assembly>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#gc_assembly> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#gencode>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-gencode" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/asn>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/blast_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#all_prots>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#seqids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat/file_in_2nd>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "compartments.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#db_gencode>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/taxid> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/taxon_db> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/asn>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#asn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-file" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/blast_full>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/blast_full_cov> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#file_in>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#sorted_aligns>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#unfilt_comp>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/seed_hits> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/gc_assembly> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/prosplign_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#tax_sql_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#max_compart_count>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_compart_count" ] ;
        sld:default       5000 ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_dump>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_dump/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_dump/seed_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#seed_hits>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/outdir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qdump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/outdir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Search Compartments, gather" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-unzip" "*" "-produce-empty-file" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl#output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl#input_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl#seed_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl#db_gencode>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-db_gencode" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int/value> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Find ProSplign Alignments, scatter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-NxM-threshold" "10000" "-affinity" "subject" "-nogenbank" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#uniColl_asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#jobs> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/asn>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#go>
        sld:type  [ sld:items  xsd:boolean ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_partial_cov>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.part_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl#file_out>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "out.asn" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "out.asn" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Align reference proteins plane complete workflow" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#go> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#tax_sql_file> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#all_prots> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#taxid> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#gc_assembly> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#align_non_match> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#align> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output_impl>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "gencode.txt" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/limit_mem>
        sld:default  "1G" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Protein Alignments, execute" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-align_filter" "pct_identity_gapopen_only >= 75" "-backlog" "1" "-comp_based_stats" "F" "-dbsize" "6000000000" "-delay" "0" "-evalue" "0.1" "-gapextend" "2" "-gapopen" "9" "-matrix" "BLOSUM62" "-max-jobs" "1" "-seg" "no" "-soft_masking" "true" "-threshold" "21" "-word_size" "6" "-nogenbank" "-short-protein-threshold" "30" ) ;
        cwl:baseCommand          ( "tblastn_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#output_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#outdir> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  4000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "unfiltered_compartments.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Seed Search Compartments" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_dump> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_wnode.cwl#asn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-file" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/sufficient_compart_length>
        sld:default  1500 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/sorted_seeds> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/blast_full_cov> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/blast_partial_cov> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "compute_gencode" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "compute_gencode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxid> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#superkingdom> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output_impl> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxon_db> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/file_in> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/align> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/align_non_match> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#full_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ofull" ] ;
        sld:default       "align_full_cov.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/sorted_seeds>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/sorted_aligns> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter Protein Seeds, compart filter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "prosplign_compart_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#unfilt_comp> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#sufficient_compart_length> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#min_prot_coverage> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#min_scaffold_coverage> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#nogenbank> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#gc_assembly> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#max_compart_count> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#compartments> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat/file_in_1st> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat/file_in_2nd> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat/file_out> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#input>
        cwl:inputBinding  [ cwl:loadContents  true ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Search Compartments, scatter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-affinity" "subject" "-batch-size" "1" "-nogenbank" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#asn> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#jobs> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/seed_hits> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/unfilt_comp> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/db_gencode>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#db_gencode> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_pro.cwl#asn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Find ProSplign Alignments, gather" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-unzip" "*" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl#input_path> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl#prosplign_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/file_in>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat/file_out> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_non_match>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#align_filter/align_non_match> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#part_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-opartial" ] ;
        sld:default       "align_partial_cov.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/gc_assembly> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/sufficient_compart_length> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/unfilt_comp> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart_filter/compartments> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_prosplign_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/seqids> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#taxid> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/blast_full> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/prosplign> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/align> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Protein_Alignments/align_non_match> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#blast_full>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump_pro.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "prosplign.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#cat/file_in_1st>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_align_filter.cwl#blast_full> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qdump.cwl#seed_align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_full_cov>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.full_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter Full-Coverage Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "bacterial_protalign_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#full_output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#sorted_seeds> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#filter_accept> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#max_extent> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#part_output> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_full_cov> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_partial_cov> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  8000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#blast_align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "blast.*.asn" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#gc_assembly>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl#file_in_1st>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        sld:default       "blastdb" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#all_prots> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#gc_assembly>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-gc-assembly" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Protein Alignments, scatter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-affinity" "subject" "-max-batch-length" "10000" "-nogenbank" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#jobs> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int/input>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode/output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#blast_aligns>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart.cwl#unfilt_comp>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#tblastn_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#value>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Search_Compartments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Filter_Protein_Seeds_prosplign_compart/seed_hits>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#seed_hits> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/db_gencode>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Compute_Gencode_int/value> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "file concatenation" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "cat" ) ;
        cwl:baseCommand          ( "cat" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl#file_in_1st> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl#file_in_2nd> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/cat.cwl#file_out> ;
        cwl:stdout               "out.asn" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output_non_match>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-non-match-output" ] ;
        sld:default       "align-nomatch.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#compart_filter_prosplign/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Sort Seed Hits, align_sort" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-ifmt" "seq-align-set" "-k" "query,subject" "-nogenbank" ) ;
        cwl:baseCommand          ( "align_sort" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#limit_mem> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#blast_aligns> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl#sorted_aligns> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/blast_aligns>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#cat/file_out> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#seqids> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Filter_Full_Coverage_Alignments/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl>
        a                          cwl:ExpressionTool ;
        ns1:original_cwlVersion    "v1.2" ;
        ExpressionTool:expression  "${ return { \"value\": parseInt(inputs.input.contents) }; }\n" ;
        cwl:cwlVersion             cwl:v1.2 ;
        cwl:inputs                 <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#input> ;
        cwl:outputs                <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#value> ;
        cwl:requirements           [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/blast_aligns> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/limit_mem> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/uniColl_asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Sort_Seed_Hits/sorted_aligns> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_sort.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/prosplign_compart_filter.cwl#min_prot_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-min_prot_coverage" ] ;
        sld:default       5e-02 ;
        sld:type          xsd:float .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#Seed_Protein_Alignments/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#Find_ProSplign_Alignments_gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_compart_filter_prosplign.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed.cwl#asn_cache>
        sld:type  cwl:Directory .