{"@id":"https://w3id.org/cwl/view/git/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","retrievedFrom":{"repoUrl":"https://github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial.git","branch":"080063b7443c98bc378935e16f747f8c542c9521","path":"FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","url":"https://github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial/blob/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl"},"retrievedOn":"2023-01-09T09:54:49.847+00:00","lastCommit":"080063b7443c98bc378935e16f747f8c542c9521","label":"FragPipe: TMT Integrator and QC","doc":"This workflow step executes TMT-Integrator using the report tables generated by Philosopher. The program applies a series of statistical filters, and high-quality thresholds to filter the data. Summary report tables are created containing peptides, proteins, genes, and phosphosites (only for phospho-enriched data sets).","inputs":{"database":{"type":"File"},"psm_file":{"type":"File[]"}},"outputs":{"tmt_qc_report":{"label":"TMT QC Report","type":"File (Optional)"},"all_report_files":{"type":"File[] (Optional)"}},"steps":{},"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    \"psm_file\" [fillcolor=\"#94DDF4\",label=\"psm_file\"];\n    \"database\" [fillcolor=\"#94DDF4\",label=\"database\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"all_report_files\" [fillcolor=\"#94DDF4\",label=\"all_report_files\"];\n    \"tmt_qc_report\" [fillcolor=\"#94DDF4\",label=\"TMT QC Report\"];\n  }\n  \"tmt_integrator\" -> \"tmt_integrator_qc\" [label=\"tmt_gene_report\"];\n  \"psm_file\" -> \"tmt_integrator\" [label=\"psm_file\"];\n  \"database\" -> \"tmt_integrator\" [label=\"database\"];\n  \"tmt_integrator\" -> \"all_report_files\";\n  \"tmt_integrator_qc\" -> \"tmt_qc_report\";\n}\n","visualisationPng":"/graph/png/github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial/blob/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","roBundle":"/robundle/github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial/blob/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","visualisationSvg":"/graph/svg/github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial/blob/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","visualisationXdot":"/graph/xdot/github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial/blob/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","permalink":"https://w3id.org/cwl/view/git/080063b7443c98bc378935e16f747f8c542c9521/FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl","packed":false}