Mercurial > repos > galaxyp > maxquant
diff test-data/10/mqpar.xml @ 15:97a7f34fcb6a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
| author | galaxyp |
|---|---|
| date | Wed, 11 Aug 2021 09:24:23 +0000 |
| parents | |
| children | 8934bc76bb52 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10/mqpar.xml Wed Aug 11 09:24:23 2021 +0000 @@ -0,0 +1,481 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>/tmp/tmps9fy8_y6/files/0/d/3/dataset_0d32c02a-47ca-47c8-83b6-1e955f377a96.dat</fastaFilePath> + <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> + <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>revert</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>True</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>False</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <ibaq>False</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.01</peptideFdr> + <proteinFdr>0.01</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>1</minUniquePeptides> + <useCounterparts>True</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> + <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> + <alignmentTimeWindow>0</alignmentTimeWindow> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>1</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeDiaFragmentTable>False</writeDiaFragmentTable> + <writeMzTab>False</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>templateSession</name> + <maxQuantVersion>1.6.17.0</maxQuantVersion> + <pluginFolder/> + <numThreads>1</numThreads> + <batchSize>1</batchSize> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79769313486232E+308</fullMinMz> + <fullMaxMz>1.79769313486232E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>True</useDotNetCore> + <profilePerformance>False</profilePerformance> + <filePaths> + <string>/tmp/tmps9fy8_y6/job_working_directory/000/3/working/thermo.raw.thermo.raw</string> + </filePaths> + <experiments> + <string>thermo.raw.thermo.raw</string> + </experiments> + <fractions> + <short>32767</short> + </fractions> + <ptms> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + </paramGroupIndices> + <referenceChannel> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <lfqTopNPeptides>0</lfqTopNPeptides> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>1</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThresholdMs1>0</intensityThresholdMs1> + <intensityThresholdMs2>0</intensityThresholdMs2> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Standard</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>1</lfqMode> + <lfqNormClusterSize>80</lfqNormClusterSize> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>0</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>1</maxMissedCleavages> + <multiplicity>1</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + <string>Carbamidomethyl (C)</string> + </fixedModifications> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>NaN</reporterMassTolerance> + <reporterPif>NaN</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>NaN</reporterFraction> + <reporterBasePeakRatio>NaN</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crossLinkingType>0</crossLinkingType> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPaths> + </diaLibraryPaths> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>1.99</diaMinScore> + <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> + <diaXgBoostSubSample>0.9</diaXgBoostSubSample> + <centroidPosition>0</centroidPosition> + <diaQuantMethod>7</diaQuantMethod> + <diaFeatureQuantMethod>2</diaFeatureQuantMethod> + <lfqNormType>1</lfqNormType> + <diaTopNForQuant>10</diaTopNForQuant> + <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> + <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> + <diaPrecursorFilterType>0</diaPrecursorFilterType> + <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> + <diaMinPrecursorScore>0.5</diaMinPrecursorScore> + <diaMinProfileCorrelation>0</diaMinProfileCorrelation> + <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> + <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> + <diaXgBoostEstimators>580</diaXgBoostEstimators> + <diaXgBoostGamma>0.9</diaXgBoostGamma> + <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> + <diaGlobalMl>True</diaGlobalMl> + <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> + <diaMassWindowFactor>3.3</diaMassWindowFactor> + <diaRtPrediction>False</diaRtPrediction> + <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> + <diaNoMl>False</diaNoMl> + <diaPermuteRt>False</diaPermuteRt> + <diaPermuteCcs>False</diaPermuteCcs> + <diaBackgroundSubtraction>False</diaBackgroundSubtraction> + <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> + <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> + <diaLfqWeightedMedian>False</diaLfqWeightedMedian> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +