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

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

<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/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/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/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/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/tblastn_wnode_db.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<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/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_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/wf_seed_seqids.cwl#db_gencode>
        sld:type  xsd:int .

<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_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/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_seed_seqids.cwl#seqids>
        sld:type  cwl:File .

<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_seed_seqids.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<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/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_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/gpx_qsubmit_seqids.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<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_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/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/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_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/gpx_qsubmit_seqids.cwl#seqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File .

<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/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        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<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>
        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:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  4000
                                 ] .

<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/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/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/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/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_seed_seqids.cwl#asn_cache>
        sld:type  cwl:Directory .

<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/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/tblastn_wnode_db.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .