Mercurial > repos > pieterlukasse > prims_workflows
view PRIMS_iTRAQ_labeled_data.ga @ 1:4719f745bf02 default tip
setting the correct dependencies to main toolshed
author | pieter.lukasse@wur.nl |
---|---|
date | Wed, 08 Jan 2014 16:38:32 +0100 |
parents | b3ccb17adda3 |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "PRIMS- (iTRAQ) labeled data", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 200 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "", "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 320 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": { "database": { "id": 0, "output_name": "output" }, "fileType|inputFile": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool X!Tandem", "name": "precursor_mass_tolerance_lower" }, { "description": "runtime parameter for tool X!Tandem", "name": "precursor_mass_tolerance_upper" }, { "description": "runtime parameter for tool X!Tandem", "name": "precursor_error_units" } ], "name": "X!Tandem", "outputs": [ { "name": "outputFile", "type": "bioml" }, { "name": "htmlReportFile", "type": "html" }, { "name": "outTsv", "type": "tabular" } ], "position": { "left": 422, "top": 199 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_xtandem200/2.0.0", "tool_state": "{\"__page__\": 0, \"fragment_error_units\": \"\\\"Daltons\\\"\", \"precursor_mass_tolerance_lower\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"database\": \"null\", \"minimum_fragment_mz\": \"\\\"150\\\"\", \"fileType\": \"{\\\"type\\\": \\\"fileSet\\\", \\\"__current_case__\\\": 1, \\\"inputFile\\\": null}\", \"potential_modifications\": \"[\\\"45.987721@C\\\", \\\"144.102063@[\\\", \\\"144.102063@K\\\"]\", \"cleavage_site\": \"\\\"[RK]|{P}\\\"\", \"maximum_missed_cleavage_sites\": \"\\\"1\\\"\", \"fixed_modifications\": \"\\\"45.987721@C,144.102063@[,144.102063@K\\\"\", \"refinementOpt\": \"{\\\"refinement\\\": \\\"yes\\\", \\\"refine_potential_modifications\\\": null, \\\"refine_max_valid_expect\\\": \\\"0.01\\\", \\\"__current_case__\\\": 0, \\\"refine_point_mutation\\\": \\\"yes\\\"}\", \"max_valid_expect\": \"\\\"0.1\\\"\", \"precursor_mass_tolerance_upper\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragment_mass_tolerance\": \"\\\"0.6\\\"\", \"precursor_error_units\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reverse_scoring\": \"\\\"no\\\"\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "2.0.0", "type": "tool", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "fileType|inputFormatType|inputFile": { "id": 2, "output_name": "outputFile" } }, "inputs": [], "name": "DB search converter", "outputs": [ { "name": "outputFile", "type": "mzid" } ], "position": { "left": 640, "top": 200 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_dbsearch_converter/1.0.1", "tool_state": "{\"__page__\": 0, \"fileType\": \"{\\\"inputFormatType\\\": {\\\"isMs2SpectrumIdStartingAtZero\\\": \\\"true\\\", \\\"inputFormat\\\": \\\"xtandem\\\", \\\"__current_case__\\\": 0, \\\"inputFile\\\": null}, \\\"type\\\": \\\"fileSet\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "ppidsFileName": { "id": 3, "output_name": "outputFile" }, "spectraDataFile": { "id": 1, "output_name": "output" } }, "inputs": [], "name": "Quantiline", "outputs": [ { "name": "outputFile", "type": "apml" }, { "name": "outReport", "type": "html" } ], "position": { "left": 860, "top": 200 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantiline1/1.0.2", "tool_state": "{\"ppidsFileName\": \"null\", \"__page__\": 0, \"labelMzValues\": \"\\\"114.0,115.0,116.0,117.0\\\"\", \"__rerun_remap_job_id__\": null, \"spectraDataFile\": \"null\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"labelmTol\": \"\\\"0.5\\\"\"}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "5": { "annotation": "", "id": 5, "input_connections": { "annotationSourceFiles_0|identificationsFile": { "id": 3, "output_name": "outputFile" }, "annotationSourceFiles_0|spectraFile": { "id": 1, "output_name": "output" }, "apmlFile": { "id": 4, "output_name": "outputFile" } }, "inputs": [], "name": "MsFilt", "outputs": [ { "name": "outputApml", "type": "apml" }, { "name": "outNewIdsApml", "type": "apml" }, { "name": "outputCSV", "type": "csv" }, { "name": "outRankingTable", "type": "csv" }, { "name": "outProteinCoverageCSV", "type": "csv" }, { "name": "htmlReportFile", "type": "html" } ], "position": { "left": 1080, "top": 200 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/msfilt/1.0.2", "tool_state": "{\"annotationSourceFiles\": \"[{\\\"identificationsFile\\\": null, \\\"__index__\\\": 0, \\\"spectraFile\\\": null}]\", \"filterOutFPIds\": \"\\\"True\\\"\", \"filterOutFPAnnotations\": \"\\\"True\\\"\", \"addRawIntensityInfo\": \"\\\"False\\\"\", \"addScaledIntensityInfo\": \"\\\"False\\\"\", \"__page__\": 0, \"apmlFile\": \"null\", \"fpCriteriaExpression\": \"\\\"qmDRT <0 or qmDMA <-0.5 or (qmDMP <-0.5 and qmBSCR<-0.5) or (!isNaN(smXTD) and smXTD >0.01)\\\"\", \"statisticalMeasuresConfig\": \"\\\"smXTD => MS:1001330,XSLASH!Tandem:expect,min \\\\r\\\\npvCSVEX => p_value,CSV_EXPORT,min \\\\r\\\\nsmAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max \\\\r\\\\nsmLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max \\\"\", \"rankingWeightConfig\": \"\\\"qmDRT => delta rt (standard score),1 \\\\r\\\\nqmDMA => delta mass annotation (standard score),1 \\\\r\\\\nqmDMP => delta mass psm (standard score),1 \\\\r\\\\nqmBSCR => best peptide score (standard score),1 \\\\r\\\\nqmALCV => alignment coverage (fraction),1 \\\\r\\\\nqmSTCV => score type coverage (fraction),1 \\\\r\\\\nqmPACV => peptide's best proteinAnnotCoverage (standard score),1 \\\\r\\\\nqmPICV => peptide's best proteinIdentifCoverage (standard score),1 \\\\r\\\\nqmANS => annotation sources (count),1 \\\\r\\\\nqmCSEV => charge states evidence (count),0.2 \\\\r\\\\nqmBCSP=> best correlation with source or product peptide (correl),1 \\\\r\\\\nqmBCCS => best correlation with other charge state (correl),1 \\\\r\\\\nqmBCOS => best correlation with other sibling peptide (correl),1 \\\"\", \"addRawRankingInfo\": \"\\\"False\\\"\", \"fpCriteriaExpressionForIds\": \"\\\"(qmDMP <-0.5 and qmBSCR<-0.5) or (!isNaN(smXTD) and smXTD >0.01)\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"filterOutUnannotatedAlignments\": \"\\\"True\\\"\"}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "6": { "annotation": "", "id": 6, "input_connections": { "annotatedQuantificationFiles_0|annotatedQuantificationFile": { "id": 5, "output_name": "outputApml" }, "identificationFiles_0|identificationFile": { "id": 5, "output_name": "outNewIdsApml" } }, "inputs": [], "name": "Quantifere", "outputs": [ { "name": "outputCSV", "type": "csv" }, { "name": "outputInferenceLogCSV", "type": "csv" }, { "name": "htmlReportFile", "type": "html" }, { "name": "outputSummaryAnnotationCSV", "type": "csv" } ], "position": { "left": 1300, "top": 200 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantifere1/1.0.2", "tool_state": "{\"__page__\": 0, \"identificationFiles\": \"[{\\\"__index__\\\": 0, \\\"identificationFile\\\": null}]\", \"quantificationDataToUse\": \"\\\"auto\\\"\", \"minAboveAverageHits\": \"\\\"1\\\"\", \"statisticalMeasuresConfig\": \"\\\"smXTD => MS:1001330,XSLASH!Tandem:expect,min \\\\r\\\\npvCSVEX => p_value,CSV_EXPORT,min \\\\r\\\\nsmAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max \\\\r\\\\nsmLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max \\\"\", \"annotatedQuantificationFiles\": \"[{\\\"__index__\\\": 0, \\\"annotatedQuantificationFile\\\": null}]\", \"refineModel\": \"\\\"True\\\"\", \"minProtCoverage\": \"\\\"5.0\\\"\", \"minNrIdsForInferencePeptide\": \"\\\"1\\\"\", \"functionalAnnotationCSV\": \"null\", \"minCorrel\": \"\\\"0.85\\\"\", \"summaryReport\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"is2D_LC_MS\": \"{\\\"fractions\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "7": { "annotation": "", "id": 7, "input_connections": { "csvDataFile": { "id": 6, "output_name": "outputInferenceLogCSV" } }, "inputs": [], "name": "CytoExport", "outputs": [ { "name": "htmlReportFile", "type": "html" }, { "name": "cysOutFile", "type": "cys" }, { "name": "logFile", "type": "txt" } ], "position": { "left": 1520, "top": 200 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/primv_visualization/cytoexport1/1.0.2", "tool_state": "{\"__page__\": 0, \"csvDataFile\": \"null\", \"__rerun_remap_job_id__\": null, \"configInputMode\": \"{\\\"vizMapPropsFile\\\": \\\"/com/pri/cytoexport/resources/quantifere_network_layout.props\\\", \\\"type\\\": \\\"existingTemplate\\\", \\\"alternativeTableImportJsonFile\\\": \\\"/com/pri/cytoexport/resources/quantifere_network_config.json\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"vizStyleName\": \"\\\"default\\\"\"}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] } } }