{"@id":"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/MG-RAST/pipeline.git","branch":"f5839797da8209a9d3e441023f88130219751020","path":"CWL/Workflows/index_sim_seq.workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/MG-RAST/pipeline/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","url":"https://github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl"},"retrievedOn":"2023-04-02T04:13:22.407+00:00","lastCommit":"f5839797da8209a9d3e441023f88130219751020","label":"index sim seq","doc":"create sorted / filtered similarity file with feature sequences, and index by md5","inputs":{"jobid":{"type":"String"},"clustMaps":{"type":"File[]"},"filterSims":{"type":"File[]"},"featureSeqs":{"type":"File[]"}},"outputs":{"indexOut":{"type":"File"},"simSeqOut":{"type":"File"}},"steps":{"catSeqs":{"label":"GNU cat","doc":"Concatenate FILE(s) to standard output","run":"../Tools/cat.tool.cwl","runType":"COMMANDLINETOOL","sources":{"catSeqs":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/files":{"sourceIDs":["featureSeqs"]}}},"sortSeqs":{"label":"seqUtil","doc":"Utility tool for various sequence file transformations.\n","run":"../Tools/seqUtil.tool.cwl","runType":"COMMANDLINETOOL","sources":{"sortSeqs":{"sourceIDs":["catSeqs"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/sequences":{"sourceIDs":["catSeqs"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/sortbyid2tab":{"defaultVal":"true"}}},"sortSims":{"label":"GNU sort","doc":"sort text file base on given field(s)","run":"../Tools/sort.tool.cwl","runType":"COMMANDLINETOOL","sources":{"sortSims":{"sourceIDs":["unclusterSims"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/input":{"sourceIDs":["unclusterSims"]}}},"addSeq2Sim":{"label":"uncluster sims","doc":"append feature sequence to each hit line of similarity file\n>add_seq2sims --seq_file --in_sim \n","run":"../Tools/add_seq2sims.tool.cwl","runType":"COMMANDLINETOOL","sources":{"addSeq2Sim":{"sourceIDs":["sortSims"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/outName":{"sourceIDs":["sortSims"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/sequences":{"sourceIDs":["sortSeqs"]}}},"sortSimSeq":{"label":"GNU sort","doc":"sort text file base on given field(s)","run":"../Tools/sort.tool.cwl","runType":"COMMANDLINETOOL","sources":{"sortSimSeq":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/input":{"sourceIDs":["addSeq2Sim"]}}},"indexSimSeq":{"label":"index sims by md5","doc":"index m8 format blast file by 2nd column (sorted required)\nreturn: value, seek, length for each record\n>index_sims_file_md5 --in_file <input> --out_file <outName> --md5_num <number>\n","run":"../Tools/index_sims_file_md5.tool.cwl","runType":"COMMANDLINETOOL","sources":{"indexSimSeq":{"sourceIDs":["sortSimSeq"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/outName":{"sourceIDs":["sortSimSeq"]}}},"unclusterSims":{"label":"uncluster sims","doc":"expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member\n>uncluster_sims.py <input> <outName> --cfile <cluster> --position <position>\n","run":"../Tools/uncluster_sims.tool.cwl","runType":"COMMANDLINETOOL","sources":{"unclusterSims":{"sourceIDs":["clustMaps"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/simHit":{"sourceIDs":["filterSims"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/outName":{"sourceIDs":["jobid"]}}}},"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    \"clustMaps\" [fillcolor=\"#94DDF4\",label=\"clustMaps\"];\n    \"filterSims\" [fillcolor=\"#94DDF4\",label=\"filterSims\"];\n    \"jobid\" [fillcolor=\"#94DDF4\",label=\"jobid\"];\n    \"featureSeqs\" [fillcolor=\"#94DDF4\",label=\"featureSeqs\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"simSeqOut\" [fillcolor=\"#94DDF4\",label=\"simSeqOut\"];\n    \"indexOut\" [fillcolor=\"#94DDF4\",label=\"indexOut\"];\n  }\n  \"unclusterSims\" [label=\"uncluster sims\"];\n  \"sortSeqs\" [label=\"seqUtil\"];\n  \"sortSimSeq\" [label=\"GNU sort\"];\n  \"indexSimSeq\" [label=\"index sims by md5\"];\n  \"addSeq2Sim\" [label=\"uncluster sims\"];\n  \"catSeqs\" [label=\"GNU cat\"];\n  \"sortSims\" [label=\"GNU sort\"];\n  \"clustMaps\" -> \"unclusterSims\" [label=\"clustMap\"];\n  \"filterSims\" -> \"unclusterSims\" [label=\"simHit\"];\n  \"jobid\" -> \"unclusterSims\" [label=\"outName\"];\n  \"catSeqs\" -> \"sortSeqs\" [label=\"output\"];\n  \"catSeqs\" -> \"sortSeqs\" [label=\"sequences\"];\n  \"default1\" -> \"sortSeqs\" [label=\"sortbyid2tab\"];\n  \"default1\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"jobid\" -> \"sortSimSeq\" [label=\"outName\"];\n  \"addSeq2Sim\" -> \"sortSimSeq\" [label=\"input\"];\n  \"sortSimSeq\" -> \"indexSimSeq\" [label=\"input\"];\n  \"sortSimSeq\" -> \"indexSimSeq\" [label=\"outName\"];\n  \"sortSims\" -> \"addSeq2Sim\" [label=\"similarity\"];\n  \"sortSeqs\" -> \"addSeq2Sim\" [label=\"sequences\"];\n  \"sortSims\" -> \"addSeq2Sim\" [label=\"outName\"];\n  \"jobid\" -> \"catSeqs\" [label=\"outName\"];\n  \"featureSeqs\" -> \"catSeqs\" [label=\"files\"];\n  \"unclusterSims\" -> \"sortSims\" [label=\"outName\"];\n  \"unclusterSims\" -> \"sortSims\" [label=\"input\"];\n  \"sortSimSeq\" -> \"simSeqOut\";\n  \"indexSimSeq\" -> \"indexOut\";\n}\n","licenseLink":"https://spdx.org/licenses/BSD-2-Clause","permalink":"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","visualisationPng":"/graph/png/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","visualisationSvg":"/graph/svg/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","roBundle":"/robundle/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl","licenseName":"BSD 2-clause \"Simplified\" License"}