{"@id":"https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","retrievedFrom":{"repoUrl":"https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git","branch":"56dafa4dab5892c5afa35713563dddc78ec5a00d","path":"tools/SSU-from-tablehits.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ProteinsWebTeam/ebi-metagenomics-cwl/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","url":"https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl"},"retrievedOn":"2023-01-04T03:00:07.223+00:00","lastCommit":"56dafa4dab5892c5afa35713563dddc78ec5a00d","label":"SSU-from-tablehits.cwl","inputs":{"table_hits":{"label":"output of infernal's cmscan or cmsearch","type":"File"}},"outputs":{"SSU_coordinates":{"type":"File"}},"steps":{"grep":{"run":"pull-SSUs.cwl","runType":"COMMANDLINETOOL","sources":{"grep":{"sourceIDs":["table_hits"]}}},"extract_coords":{"doc":"The awk script takes the output of Infernal's cm{scan,search} fmt=2 mode and\nmakes it suitable for use by esl-sfetch, a sequence selector\n\nReading the user's guide for Infernal, Version 1.1.2; July 2016\nhttp://eddylab.org/infernal/Userguide.pdf#page=60 we see that\nthe relevant fields in the cmscan output are:\n(fmt2 column number: explanation)\n3: The accession of the target sequence or profile, or ’-’ if none\n4: The name of the query sequence or profile \n10: The start of the alignment of this hit with respect to the\n    sequence, numbered 1..L for a sequence of L residues.\n11: The end of the alignment of this hit with respect to the sequence,\n    numbered 1..L for a sequence of L residues\n\nLikewise the format esl-sfetch wants is: <newname> <from> <to> <source seqname>\n\nPutting it all together we see that the newname (which esl-sfetch with\noutput using) is a concatenation of the original name, the sequence\nnumber, and the coordinates.\n","run":"extract-coords-from-cmscan.cwl","runType":"COMMANDLINETOOL","sources":{"extract_coords":{"sourceIDs":["grep"]}}}},"cwltoolVersion":"3.1.20221201130942","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    \"table_hits\" [fillcolor=\"#94DDF4\",label=\"output of infernal's cmscan or cmsearch\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"SSU_coordinates\" [fillcolor=\"#94DDF4\",label=\"SSU_coordinates\"];\n  }\n  \"extract_coords\" [label=\"extract_coords\"];\n  \"grep\" [label=\"grep\"];\n  \"grep\" -> \"extract_coords\" [label=\"infernal_matches\"];\n  \"table_hits\" -> \"grep\" [label=\"hits\"];\n  \"extract_coords\" -> \"SSU_coordinates\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","visualisationPng":"/graph/png/github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","visualisationSvg":"/graph/svg/github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","roBundle":"/robundle/github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl","licenseName":"Apache License 2.0"}