Mercurial > repos > galaxyp > maxquant

diff test-data/05/mqpar.xml @ 10:f522c08e900c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
author galaxyp
date Fri, 12 Mar 2021 08:41:06 +0000
parents
children 0839f84def5e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/05/mqpar.xml	Fri Mar 12 08:41:06 2021 +0000
@@ -0,0 +1,451 @@
+<?xml version="1.0" ?>
+<MaxQuantParams>
+	<fastaFiles>
+		<FastaFileInfo>
+			<fastaFilePath>/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat</fastaFilePath>
+			<identifierParseRule>^&gt;.*\|(.*)\|.*$</identifierParseRule>
+			<descriptionParseRule>^&gt;.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule>
+			<taxonomyParseRule/>
+			<variationParseRule/>
+			<modificationParseRule/>
+			<taxonomyId/>
+		</FastaFileInfo>
+	</fastaFiles>
+	<fastaFilesProteogenomics>
+   </fastaFilesProteogenomics>
+	<fastaFilesFirstSearch>
+   </fastaFilesFirstSearch>
+	<fixedSearchFolder/>
+	<andromedaCacheSize>350000</andromedaCacheSize>
+	<advancedRatios>True</advancedRatios>
+	<pvalThres>0.005</pvalThres>
+	<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
+	<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
+	<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>True</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>
+	<msmsConnection>False</msmsConnection>
+	<ibaq>True</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>0.7</matchingTimeWindow>
+	<matchingIonMobilityWindow>0.05</matchingIonMobilityWindow>
+	<alignmentTimeWindow>20</alignmentTimeWindow>
+	<alignmentIonMobilityWindow>1</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>True</writeAccumulatedPasefMsmsScansTable>
+	<writeMs3ScansTable>True</writeMs3ScansTable>
+	<writeAllPeptidesTable>True</writeAllPeptidesTable>
+	<writeMzRangeTable>True</writeMzRangeTable>
+	<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>1.6.10.43</maxQuantVersion>
+	<tempFolder/>
+	<pluginFolder/>
+	<numThreads>1</numThreads>
+	<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>False</useDotNetCore>
+	<filePaths>
+		<string>/tmp/tmp0wswhy4o/job_working_directory/000/7/working/BSA_min_22.mzxml</string>
+	</filePaths>
+	<experiments>
+		<string>BSA_min_22.mzxml</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>
+	<parameterGroups>
+		<parameterGroup>
+			<msInstrument>0</msInstrument>
+			<maxCharge>7</maxCharge>
+			<minPeakLen>2</minPeakLen>
+			<diaMinPeakLen>2</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>
+			<intensityThreshold>0</intensityThreshold>
+			<labelMods>
+				<string/>
+			</labelMods>
+			<lcmsRunType>Standard</lcmsRunType>
+			<reQuantify>False</reQuantify>
+			<lfqMode>1</lfqMode>
+			<lfqSkipNorm>True</lfqSkipNorm>
+			<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>
+			<crosslinkSearch>False</crosslinkSearch>
+			<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>
+			<diaLibraryPath/>
+			<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>2.99</diaMinScore>
+			<diaPrecursorQuant>False</diaPrecursorQuant>
+			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
+		</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>
+