{"@id":"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"681555881cbdf95a1f4c29f6dc272eb6ca8e4d60","path":"wf_bacterial_prot_src.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","url":"https://github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl"},"retrievedOn":"2026-08-30T14:21:05.174+00:00","lastCommit":"681555881cbdf95a1f4c29f6dc272eb6ca8e4d60","label":"Get Proteins","inputs":{"taxid":{"type":"Integer"},"blastdb_dir":{"type":"Directory"},"tax_sql_file":{"type":"File"},"naming_sqlite":{"type":"File"},"uniColl_asn_cache":{"type":"Directory"},"all_order_specific_blastdb":{"type":"String[]"}},"outputs":{"all_prots":{"type":"File"},"selected_blastdb":{"type":"String[]"},"universal_clusters":{"type":"File"}},"steps":{"File2Basenames":{"run":"progs/file2basenames.cwl","runType":"EXPRESSIONTOOL","sources":{"File2Basenames":{"sourceIDs":["Get_Proteins_app"]}}},"Get_Proteins_app":{"label":"Get Proteins, bacterial_prot_src","run":"protein_alignment/bacterial_prot_src.cwl","runType":"COMMANDLINETOOL","sources":{"Get_Proteins_app":{"sourceIDs":["blastdb_dir"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/tax_sql_file":{"sourceIDs":["tax_sql_file"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/naming_sqlite":{"sourceIDs":["naming_sqlite"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/uniColl_asn_cache":{"sourceIDs":["uniColl_asn_cache"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl#Get_Proteins_app/all_order_specific_blastdb":{"sourceIDs":["all_order_specific_blastdb"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"taxid\" [fillcolor=\"#94DDF4\",label=\"taxid\"];\n    \"blastdb_dir\" [fillcolor=\"#94DDF4\",label=\"blastdb_dir\"];\n    \"all_order_specific_blastdb\" [fillcolor=\"#94DDF4\",label=\"all_order_specific_blastdb\"];\n    \"uniColl_asn_cache\" [fillcolor=\"#94DDF4\",label=\"uniColl_asn_cache\"];\n    \"tax_sql_file\" [fillcolor=\"#94DDF4\",label=\"tax_sql_file\"];\n    \"naming_sqlite\" [fillcolor=\"#94DDF4\",label=\"naming_sqlite\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"universal_clusters\" [fillcolor=\"#94DDF4\",label=\"universal_clusters\"];\n    \"all_prots\" [fillcolor=\"#94DDF4\",label=\"all_prots\"];\n    \"selected_blastdb\" [fillcolor=\"#94DDF4\",label=\"selected_blastdb\"];\n  }\n  \"File2Basenames\" [label=\"File2Basenames\"];\n  \"Get_Proteins_app\" [label=\"Get Proteins, bacterial_prot_src\"];\n  \"Get_Proteins_app\" -> \"File2Basenames\" [label=\"input\"];\n  \"blastdb_dir\" -> \"Get_Proteins_app\" [label=\"blastdb_dir\"];\n  \"taxid\" -> \"Get_Proteins_app\" [label=\"taxid\"];\n  \"uniColl_asn_cache\" -> \"Get_Proteins_app\" [label=\"uniColl_asn_cache\"];\n  \"tax_sql_file\" -> \"Get_Proteins_app\" [label=\"tax_sql_file\"];\n  \"naming_sqlite\" -> \"Get_Proteins_app\" [label=\"naming_sqlite\"];\n  \"all_order_specific_blastdb\" -> \"Get_Proteins_app\" [label=\"all_order_specific_blastdb\"];\n  \"Get_Proteins_app\" -> \"universal_clusters\";\n  \"Get_Proteins_app\" -> \"all_prots\";\n  \"File2Basenames\" -> \"selected_blastdb\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_bacterial_prot_src.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/LICENSE.md"}