{"@id":"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"22ffe27d9d4a899def7592d75d5871c1856adbdb","path":"prepare_user_input2.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","url":"https://github.com/ncbi/pgap/blob/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl"},"retrievedOn":"2026-09-01T15:58:48.487+00:00","lastCommit":"22ffe27d9d4a899def7592d75d5871c1856adbdb","label":"Prepare user input","doc":"Prepare user input for  NCBI-PGAP pipeline","inputs":{"fasta":{"type":"File"},"submol":{"type":"File"},"taxon_db":{"type":"File"},"no_internet":{"type":"Boolean (Optional)"},"ignore_all_errors":{"type":"Boolean (Optional)"}},"outputs":{"taxid":{"type":"Integer"},"input_asn_type":{"type":"String"},"output_entries":{"type":"File (Optional)"},"locus_tag_prefix":{"type":"String"},"output_seq_submit":{"type":"File (Optional)"},"submol_block_json":{"type":"File"}},"steps":{"yaml2json":{"label":"yaml2json","run":"progs/yaml2json.cwl","runType":"COMMANDLINETOOL","sources":{"yaml2json":{"sourceIDs":["submol"]}}},"file2int_taxid":{"run":"progs/file2int.cwl","runType":"EXPRESSIONTOOL","sources":{"file2int_taxid":{"sourceIDs":["pgapx_yaml_ctl"]}}},"pgapx_yaml_ctl":{"label":"pgapx_yaml_ctl","doc":"Converts input JSON file to ASN.1 template","run":"progs/pgapx_yaml_ctl.cwl","runType":"COMMANDLINETOOL","sources":{"pgapx_yaml_ctl":{"sourceIDs":["ignore_all_errors"]},"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input":{"sourceIDs":["yaml2json"]},"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db":{"sourceIDs":["taxon_db"]},"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta":{"sourceIDs":["fasta"]},"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet":{"sourceIDs":["no_internet"]}}},"file2string_ltp":{"run":"progs/file2string.cwl","runType":"EXPRESSIONTOOL","sources":{"file2string_ltp":{"sourceIDs":["pgapx_yaml_ctl"]}}},"initial_cleanup":{"label":"asn_cleanup","run":"progs/asn_cleanup.cwl","runType":"COMMANDLINETOOL","sources":{"initial_cleanup":{"sourceIDs":["pgapx_yaml_ctl"]}}},"type_based_splitter":{"run":"5aaae00d2dbaa434b24e7544cfd9fd58","runType":"EXPRESSIONTOOL","sources":{"type_based_splitter":{"sourceIDs":["file2string_input_asn_type"]},"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl#type_based_splitter/input":{"sourceIDs":["initial_cleanup"]}}},"file2string_input_asn_type":{"run":"progs/file2string.cwl","runType":"EXPRESSIONTOOL","sources":{"file2string_input_asn_type":{"sourceIDs":["pgapx_yaml_ctl"]}}}},"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    \"taxon_db\" [fillcolor=\"#94DDF4\",label=\"taxon_db\"];\n    \"ignore_all_errors\" [fillcolor=\"#94DDF4\",label=\"ignore_all_errors\"];\n    \"fasta\" [fillcolor=\"#94DDF4\",label=\"fasta\"];\n    \"submol\" [fillcolor=\"#94DDF4\",label=\"submol\"];\n    \"no_internet\" [fillcolor=\"#94DDF4\",label=\"no_internet\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"output_seq_submit\" [fillcolor=\"#94DDF4\",label=\"output_seq_submit\"];\n    \"input_asn_type\" [fillcolor=\"#94DDF4\",label=\"input_asn_type\"];\n    \"output_entries\" [fillcolor=\"#94DDF4\",label=\"output_entries\"];\n    \"locus_tag_prefix\" [fillcolor=\"#94DDF4\",label=\"locus_tag_prefix\"];\n    \"taxid\" [fillcolor=\"#94DDF4\",label=\"taxid\"];\n    \"submol_block_json\" [fillcolor=\"#94DDF4\",label=\"submol_block_json\"];\n  }\n  \"pgapx_yaml_ctl\" [label=\"pgapx_yaml_ctl\"];\n  \"file2string_ltp\" [label=\"file2string_ltp\"];\n  \"yaml2json\" [label=\"yaml2json\"];\n  \"file2int_taxid\" [label=\"file2int_taxid\"];\n  \"file2string_input_asn_type\" [label=\"file2string_input_asn_type\"];\n  \"type_based_splitter\" [label=\"type_based_splitter\"];\n  \"initial_cleanup\" [label=\"asn_cleanup\"];\n  \"ignore_all_errors\" -> \"pgapx_yaml_ctl\" [label=\"ignore_all_errors\"];\n  \"taxon_db\" -> \"pgapx_yaml_ctl\" [label=\"taxon_db\"];\n  \"yaml2json\" -> \"pgapx_yaml_ctl\" [label=\"input\"];\n  \"no_internet\" -> \"pgapx_yaml_ctl\" [label=\"no_internet\"];\n  \"fasta\" -> \"pgapx_yaml_ctl\" [label=\"input_fasta\"];\n  \"pgapx_yaml_ctl\" -> \"file2string_ltp\" [label=\"input\"];\n  \"submol\" -> \"yaml2json\" [label=\"input\"];\n  \"pgapx_yaml_ctl\" -> \"file2int_taxid\" [label=\"input\"];\n  \"pgapx_yaml_ctl\" -> \"file2string_input_asn_type\" [label=\"input\"];\n  \"file2string_input_asn_type\" -> \"type_based_splitter\" [label=\"input_asn_type\"];\n  \"initial_cleanup\" -> \"type_based_splitter\" [label=\"input\"];\n  \"pgapx_yaml_ctl\" -> \"initial_cleanup\" [label=\"inp_annotation\"];\n  \"type_based_splitter\" -> \"output_seq_submit\";\n  \"file2string_input_asn_type\" -> \"input_asn_type\";\n  \"type_based_splitter\" -> \"output_entries\";\n  \"file2string_ltp\" -> \"locus_tag_prefix\";\n  \"file2int_taxid\" -> \"taxid\";\n  \"yaml2json\" -> \"submol_block_json\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/22ffe27d9d4a899def7592d75d5871c1856adbdb/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/22ffe27d9d4a899def7592d75d5871c1856adbdb/prepare_user_input2.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/22ffe27d9d4a899def7592d75d5871c1856adbdb/LICENSE.md"}