Mercurial > repos > galaxyp > peptideshaker
diff test-data/Identification_Parameters_default_modifications.par @ 55:bb0130ff73ce draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
| author | galaxyp |
|---|---|
| date | Fri, 15 Jan 2021 14:06:27 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Identification_Parameters_default_modifications.par Fri Jan 15 14:06:27 2021 +0000 @@ -0,0 +1,882 @@ +{ + "marshallableParameterType": "identification_parameters", + "version": "5.0.1", + "name": "IdentificationParametersOutput", + "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nFragment Tolerance: 0.5 Da.\n", + "defaultDescription": true, + "searchParameters": { + "version": "5.0.1", + "precursorAccuracyType": "PPM", + "fragmentAccuracyType": "DA", + "precursorTolerance": 10.0, + "fragmentIonMZTolerance": 0.5, + "modificationParameters": { + "fixedModifications": [ + "Carbamidomethylation of C" + ], + "variableModifications": [ + "Oxidation of M" + ], + "refinementVariableModifications": [], + "refinementFixedModifications": [], + "colors": {}, + "backUp": { + "Carbamidomethylation of C": { + "modificationType": "modaa", + "name": "Carbamidomethylation of C", + "shortName": "cmm", + "neutralLosses": [], + "reporterIons": [], + "pattern": { + "length": 0, + "residueTargeted": { + "0": [ + "C" + ] + }, + "id": 0 + }, + "atomChainAdded": { + "atomChain": [ + { + "atomSymbol": "C", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "C", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "H", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "H", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "H", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "N", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "O", + "isotope": 0, + "id": 0 + } + ], + "mass": -1.0, + "id": 0 + }, + "atomChainRemoved": { + "atomChain": [], + "mass": -1.0, + "id": 0 + }, + "unimodCvTerm": { + "ontology": "UNIMOD", + "accession": "UNIMOD:4", + "name": "Carbamidomethyl", + "id": 0 + }, + "psiModCvTerm": { + "ontology": "MOD", + "accession": "MOD:01060", + "name": "S-carboxamidomethyl-L-cysteine", + "id": 0 + }, + "category": "Common", + "id": 0 + }, + "Oxidation of M": { + "modificationType": 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"numberOfPeaksToKeepPerWindow": 200, + "minAllowedIntensityRatioToBasePeak": 0.01, + "normalizePeaksAcrossAllWindows": false, + "modPeptidesAreDifferent": false, + "noOneHitWonders": false, + "searchTarget": true, + "decoyType": "None", + "maxModificationIsoforms": 1024, + "minVariantDepth": 1, + "maxHeterozygousVariants": 4, + "runGptm": false, + "gPtmCategories": [ + "Common_Biological", + "Common_Artifact", + "Metal" + ], + "id": 0 + } + }, + "2": { + "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters", + "data": { + "maxEValue": 0.01, + "outputResults": "all", + "dynamicRange": 100.0, + "nPeaks": 50, + "minPrecursorMass": 500.0, + "minFragmentMz": 200.0, + "minPeaksPerSpectrum": 5, + "proteinQuickAcetyl": true, + "quickPyrolidone": true, + "refine": true, + "refineSemi": false, + "refinePointMutations": false, + "refineSpectrumSynthesis": true, + "refineUnanticipatedCleavages": true, + "refineSnaps": true, + "maximumExpectationValueRefinement": 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false, + "instrumentID": 3, + "fragmentationType": 3, + "protocol": 0, + "minPeptideLength": 8, + "maxPeptideLength": 30, + "numberOfSpectrumMarches": 10, + "additionalOutput": false, + "numberTolerableTermini": 2, + "numberOfModificationsPerPeptide": 2, + "id": 0 + } + }, + "8": { + "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters", + "data": { + "ticCutoffPercentage": 100.0, + "maxPeakCount": 100, + "numIntensityClasses": 3, + "adjustPrecursorMass": false, + "minPrecursorAdjustment": -0.5, + "maxPrecursorAdjustment": 1.5, + "precursorAdjustmentStep": 0.1, + "numChargeStates": 3, + "outputSuffix": "", + "useChargeStateFromMS": true, + "duplicateSpectra": true, + "deisotopingMode": 0, + "isotopeMzTolerance": 0.25, + "complementMzTolerance": 0.1, + "tagLength": 4, + "maxDynamicMods": 2, + "maxTagCount": 10, + "intensityScoreWeight": 1.0, + "mzFidelityScoreWeight": 1.0, + "complementScoreWeight": 1.0, + "variableModifications": [], + "id": 0 + } + }, 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+ "massAnalyzer": "FT", + "id": 0 + } + } + }, + "flanking": false, + "id": 0 + }, + "annotationParameters": { + "yAxisZoomExcludesBackgroundPeaks": true, + "showAllPeaks": false, + "intensityThresholdType": "percentile", + "intensityLimit": 0.75, + "automaticAnnotation": true, + "selectedIonsMap": { + "IMMONIUM_ION": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20 + ], + "PEPTIDE_FRAGMENT_ION": [ + 4, + 1 + ], + "PRECURSOR_ION": [ + 0 + ], + "TAG_FRAGMENT_ION": [ + 4, + 1 + ], + "REPORTER_ION": [], + "RELATED_ION": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18 + ] + }, + "neutralLossesList": [ + { + "composition": { + "atomChain": [ + { + "atomSymbol": "H", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "H", + "isotope": 0, + "id": 0 + }, + { + "atomSymbol": "O", + "isotope": 0, + "id": 0 + } + ], + "mass": -1.0, + "id": 0 + }, + "name": "H2O", + "fixed": 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true, + "simplifyGroupsConfidence": true, + "simplifyGroupsEnzymaticity": true, + "simplifyGroupsVariants": true, + "confidenceThreshold": 0.05, + "id": 0 + }, + "idValidationParameters": { + "defaultProteinFDR": 1.0, + "defaultPeptideFDR": 1.0, + "defaultPsmFDR": 1.0, + "validationQCPreferences": { + "dbSize": false, + "firstDecoy": true, + "confidenceMargin": 1.0, + "id": 0 + }, + "id": 0 + }, + "fractionParameters": { + "proteinConfidenceMwPlots": 95.0, + "fractionMolecularWeightRanges": {}, + "id": 0 + }, + "fastaParameters": { + "targetDecoy": true, + "decoyFlag": "-REVERSED", + "decoySuffix": true, + "targetDecoyFileNameTag": "_concatenated_target_decoy", + "id": 0 + }, + "id": 0 +} \ No newline at end of file