Mercurial > repos > galaxyp > maxquant
comparison test-data/05/mqpar.xml @ 21:8934bc76bb52 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
| author | galaxyp |
|---|---|
| date | Mon, 19 Jun 2023 17:02:17 +0000 |
| parents | 837224ad1694 |
| children |
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| 20:837224ad1694 | 21:8934bc76bb52 |
|---|---|
| 21 <pvalThres>0.005</pvalThres> | 21 <pvalThres>0.005</pvalThres> |
| 22 <rtShift>False</rtShift> | 22 <rtShift>False</rtShift> |
| 23 <separateLfq>False</separateLfq> | 23 <separateLfq>False</separateLfq> |
| 24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> | 24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> |
| 25 <lfqRequireMsms>True</lfqRequireMsms> | 25 <lfqRequireMsms>True</lfqRequireMsms> |
| 26 <lfqBayesQuant>False</lfqBayesQuant> | |
| 26 <decoyMode>revert</decoyMode> | 27 <decoyMode>revert</decoyMode> |
| 27 <boxCarMode>all</boxCarMode> | 28 <boxCarMode>all</boxCarMode> |
| 28 <includeContaminants>True</includeContaminants> | 29 <includeContaminants>True</includeContaminants> |
| 29 <maxPeptideMass>4600</maxPeptideMass> | 30 <maxPeptideMass>4600</maxPeptideMass> |
| 30 <epsilonMutationScore>True</epsilonMutationScore> | 31 <epsilonMutationScore>True</epsilonMutationScore> |
| 53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> | 54 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> |
| 54 <taxonomyLevel>Species</taxonomyLevel> | 55 <taxonomyLevel>Species</taxonomyLevel> |
| 55 <avalon>False</avalon> | 56 <avalon>False</avalon> |
| 56 <nModColumns>3</nModColumns> | 57 <nModColumns>3</nModColumns> |
| 57 <ibaqLogFit>False</ibaqLogFit> | 58 <ibaqLogFit>False</ibaqLogFit> |
| 59 <ibaqChargeNormalization>False</ibaqChargeNormalization> | |
| 58 <razorProteinFdr>True</razorProteinFdr> | 60 <razorProteinFdr>True</razorProteinFdr> |
| 59 <deNovoSequencing>False</deNovoSequencing> | 61 <deNovoSequencing>False</deNovoSequencing> |
| 60 <deNovoVarMods>True</deNovoVarMods> | 62 <deNovoVarMods>False</deNovoVarMods> |
| 63 <deNovoCompleteSequence>False</deNovoCompleteSequence> | |
| 64 <deNovoCalibratedMasses>False</deNovoCalibratedMasses> | |
| 65 <deNovoMaxIterations>0</deNovoMaxIterations> | |
| 66 <deNovoProteaseReward>0</deNovoProteaseReward> | |
| 67 <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof> | |
| 68 <deNovoAgPenalty>0</deNovoAgPenalty> | |
| 69 <deNovoGgPenalty>0</deNovoGgPenalty> | |
| 70 <deNovoUseComplementScore>True</deNovoUseComplementScore> | |
| 71 <deNovoUseProteaseScore>True</deNovoUseProteaseScore> | |
| 72 <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore> | |
| 73 <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore> | |
| 74 <deNovoUseA2Score>True</deNovoUseA2Score> | |
| 61 <massDifferenceSearch>False</massDifferenceSearch> | 75 <massDifferenceSearch>False</massDifferenceSearch> |
| 62 <isotopeCalc>False</isotopeCalc> | 76 <isotopeCalc>False</isotopeCalc> |
| 63 <writePeptidesForSpectrumFile/> | 77 <writePeptidesForSpectrumFile/> |
| 64 <intensityPredictionsFile> | 78 <intensityPredictionsFile> |
| 65 </intensityPredictionsFile> | 79 </intensityPredictionsFile> |
| 95 </massDifferenceMods> | 109 </massDifferenceMods> |
| 96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> | 110 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> |
| 97 <writeMsScansTable>False</writeMsScansTable> | 111 <writeMsScansTable>False</writeMsScansTable> |
| 98 <writeMsmsScansTable>True</writeMsmsScansTable> | 112 <writeMsmsScansTable>True</writeMsmsScansTable> |
| 99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> | 113 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> |
| 100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> | 114 <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> |
| 101 <writeMs3ScansTable>True</writeMs3ScansTable> | 115 <writeMs3ScansTable>True</writeMs3ScansTable> |
| 102 <writeAllPeptidesTable>True</writeAllPeptidesTable> | 116 <writeAllPeptidesTable>True</writeAllPeptidesTable> |
| 103 <writeMzRangeTable>True</writeMzRangeTable> | 117 <writeMzRangeTable>True</writeMzRangeTable> |
| 104 <writeDiaFragmentTable>False</writeDiaFragmentTable> | 118 <writeDiaFragmentTable>False</writeDiaFragmentTable> |
| 119 <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> | |
| 105 <writeMzTab>False</writeMzTab> | 120 <writeMzTab>False</writeMzTab> |
| 106 <disableMd5>False</disableMd5> | 121 <disableMd5>False</disableMd5> |
| 107 <cacheBinInds>True</cacheBinInds> | 122 <cacheBinInds>True</cacheBinInds> |
| 108 <etdIncludeB>False</etdIncludeB> | 123 <etdIncludeB>False</etdIncludeB> |
| 109 <ms2PrecursorShift>0</ms2PrecursorShift> | 124 <ms2PrecursorShift>0</ms2PrecursorShift> |
| 110 <complementaryIonPpm>20</complementaryIonPpm> | 125 <complementaryIonPpm>20</complementaryIonPpm> |
| 111 <variationParseRule/> | 126 <variationParseRule/> |
| 112 <variationMode>none</variationMode> | 127 <variationMode>none</variationMode> |
| 113 <useSeriesReporters>False</useSeriesReporters> | 128 <useSeriesReporters>False</useSeriesReporters> |
| 114 <name>templateSession</name> | 129 <name>templateSession</name> |
| 115 <maxQuantVersion>1.6.17.0</maxQuantVersion> | 130 <maxQuantVersion>2.0.3.0</maxQuantVersion> |
| 116 <pluginFolder/> | 131 <pluginFolder/> |
| 117 <numThreads>2</numThreads> | 132 <numThreads>1</numThreads> |
| 118 <batchSize>1</batchSize> | |
| 119 <emailAddress/> | 133 <emailAddress/> |
| 120 <smtpHost/> | 134 <smtpHost/> |
| 121 <emailFromAddress/> | 135 <emailFromAddress/> |
| 122 <fixedCombinedFolder/> | 136 <fixedCombinedFolder/> |
| 123 <fullMinMz>-1.79769313486232E+308</fullMinMz> | 137 <fullMinMz>-1.79769313486232E+308</fullMinMz> |
| 149 <string/> | 163 <string/> |
| 150 </referenceChannel> | 164 </referenceChannel> |
| 151 <intensPred>False</intensPred> | 165 <intensPred>False</intensPred> |
| 152 <intensPredModelReTrain>False</intensPredModelReTrain> | 166 <intensPredModelReTrain>False</intensPredModelReTrain> |
| 153 <lfqTopNPeptides>0</lfqTopNPeptides> | 167 <lfqTopNPeptides>0</lfqTopNPeptides> |
| 168 <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> | |
| 169 <diaFragChargesForQuant>1</diaFragChargesForQuant> | |
| 170 <timsRearrangeSpectra>False</timsRearrangeSpectra> | |
| 171 <gridSpacing>0.5</gridSpacing> | |
| 172 <proteinGroupingFile/> | |
| 154 <parameterGroups> | 173 <parameterGroups> |
| 155 <parameterGroup> | 174 <parameterGroup> |
| 156 <msInstrument>0</msInstrument> | 175 <msInstrument>0</msInstrument> |
| 157 <maxCharge>7</maxCharge> | 176 <maxCharge>7</maxCharge> |
| 158 <minPeakLen>2</minPeakLen> | 177 <minPeakLen>2</minPeakLen> |
| 256 <timsRemovePrecursor>True</timsRemovePrecursor> | 275 <timsRemovePrecursor>True</timsRemovePrecursor> |
| 257 <timsIsobaricLabels>False</timsIsobaricLabels> | 276 <timsIsobaricLabels>False</timsIsobaricLabels> |
| 258 <timsCollapseMsms>True</timsCollapseMsms> | 277 <timsCollapseMsms>True</timsCollapseMsms> |
| 259 <crossLinkingType>0</crossLinkingType> | 278 <crossLinkingType>0</crossLinkingType> |
| 260 <crossLinker/> | 279 <crossLinker/> |
| 261 <minMatchXl>0</minMatchXl> | 280 <minMatchXl>3</minMatchXl> |
| 262 <minPairedPepLenXl>6</minPairedPepLenXl> | 281 <minPairedPepLenXl>6</minPairedPepLenXl> |
| 282 <minScore_Dipeptide>40</minScore_Dipeptide> | |
| 283 <minScore_Monopeptide>0</minScore_Monopeptide> | |
| 284 <minScore_PartialCross>10</minScore_PartialCross> | |
| 263 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> | 285 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> |
| 286 <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor> | |
| 287 <isHybridPrecDetermination>False</isHybridPrecDetermination> | |
| 288 <topXcross>3</topXcross> | |
| 289 <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross> | |
| 264 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> | 290 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> |
| 265 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> | 291 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> |
| 266 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> | 292 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> |
| 267 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> | 293 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> |
| 268 <crosslinkModifications> | 294 <crosslinkModifications> |
| 275 </crosslinkNetworkFiles> | 301 </crosslinkNetworkFiles> |
| 276 <crosslinkMode/> | 302 <crosslinkMode/> |
| 277 <peakRefinement>False</peakRefinement> | 303 <peakRefinement>False</peakRefinement> |
| 278 <isobaricSumOverWindow>True</isobaricSumOverWindow> | 304 <isobaricSumOverWindow>True</isobaricSumOverWindow> |
| 279 <isobaricWeightExponent>0.75</isobaricWeightExponent> | 305 <isobaricWeightExponent>0.75</isobaricWeightExponent> |
| 306 <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> | |
| 280 <diaLibraryType>0</diaLibraryType> | 307 <diaLibraryType>0</diaLibraryType> |
| 281 <diaLibraryPaths> | 308 <diaLibraryPaths> |
| 282 </diaLibraryPaths> | 309 </diaLibraryPaths> |
| 283 <diaPeptidePaths> | 310 <diaPeptidePaths> |
| 284 </diaPeptidePaths> | 311 </diaPeptidePaths> |
| 321 <diaPermuteCcs>False</diaPermuteCcs> | 348 <diaPermuteCcs>False</diaPermuteCcs> |
| 322 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> | 349 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> |
| 323 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> | 350 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> |
| 324 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> | 351 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> |
| 325 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> | 352 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> |
| 353 <diaTransferQvalue>0.3</diaTransferQvalue> | |
| 354 <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> | |
| 355 <diaMinPeaksForRecal>5</diaMinPeaksForRecal> | |
| 356 <diaUseFragIntensForMl>False</diaUseFragIntensForMl> | |
| 357 <diaUseFragMassesForMl>False</diaUseFragMassesForMl> | |
| 358 <diaMaxTrainInstances>1000000</diaMaxTrainInstances> | |
| 326 </parameterGroup> | 359 </parameterGroup> |
| 327 </parameterGroups> | 360 </parameterGroups> |
| 328 <msmsParamsArray> | 361 <msmsParamsArray> |
| 329 <msmsParams> | 362 <msmsParams> |
| 330 <Name>FTMS</Name> | 363 <Name>FTMS</Name> |
| 331 <MatchTolerance>20</MatchTolerance> | 364 <MatchTolerance>20</MatchTolerance> |
| 332 <MatchToleranceInPpm>True</MatchToleranceInPpm> | 365 <MatchToleranceInPpm>True</MatchToleranceInPpm> |
| 333 <DeisotopeTolerance>7</DeisotopeTolerance> | 366 <DeisotopeTolerance>7</DeisotopeTolerance> |
| 334 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> | 367 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> |
| 335 <DeNovoTolerance>10</DeNovoTolerance> | 368 <DeNovoTolerance>25</DeNovoTolerance> |
| 336 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> | 369 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> |
| 337 <Deisotope>True</Deisotope> | 370 <Deisotope>True</Deisotope> |
| 338 <Topx>12</Topx> | 371 <Topx>12</Topx> |
| 339 <TopxInterval>100</TopxInterval> | 372 <TopxInterval>100</TopxInterval> |
| 340 <HigherCharges>True</HigherCharges> | 373 <HigherCharges>True</HigherCharges> |
| 347 <Name>ITMS</Name> | 380 <Name>ITMS</Name> |
| 348 <MatchTolerance>0.5</MatchTolerance> | 381 <MatchTolerance>0.5</MatchTolerance> |
| 349 <MatchToleranceInPpm>False</MatchToleranceInPpm> | 382 <MatchToleranceInPpm>False</MatchToleranceInPpm> |
| 350 <DeisotopeTolerance>0.15</DeisotopeTolerance> | 383 <DeisotopeTolerance>0.15</DeisotopeTolerance> |
| 351 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> | 384 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> |
| 352 <DeNovoTolerance>0.25</DeNovoTolerance> | 385 <DeNovoTolerance>0.5</DeNovoTolerance> |
| 353 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> | 386 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> |
| 354 <Deisotope>False</Deisotope> | 387 <Deisotope>False</Deisotope> |
| 355 <Topx>8</Topx> | 388 <Topx>8</Topx> |
| 356 <TopxInterval>100</TopxInterval> | 389 <TopxInterval>100</TopxInterval> |
| 357 <HigherCharges>True</HigherCharges> | 390 <HigherCharges>True</HigherCharges> |
| 364 <Name>TOF</Name> | 397 <Name>TOF</Name> |
| 365 <MatchTolerance>40</MatchTolerance> | 398 <MatchTolerance>40</MatchTolerance> |
| 366 <MatchToleranceInPpm>True</MatchToleranceInPpm> | 399 <MatchToleranceInPpm>True</MatchToleranceInPpm> |
| 367 <DeisotopeTolerance>0.01</DeisotopeTolerance> | 400 <DeisotopeTolerance>0.01</DeisotopeTolerance> |
| 368 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> | 401 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> |
| 369 <DeNovoTolerance>0.02</DeNovoTolerance> | 402 <DeNovoTolerance>25</DeNovoTolerance> |
| 370 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> | 403 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> |
| 371 <Deisotope>True</Deisotope> | 404 <Deisotope>True</Deisotope> |
| 372 <Topx>10</Topx> | 405 <Topx>10</Topx> |
| 373 <TopxInterval>100</TopxInterval> | 406 <TopxInterval>100</TopxInterval> |
| 374 <HigherCharges>True</HigherCharges> | 407 <HigherCharges>True</HigherCharges> |
| 375 <IncludeWater>True</IncludeWater> | 408 <IncludeWater>True</IncludeWater> |
| 381 <Name>Unknown</Name> | 414 <Name>Unknown</Name> |
| 382 <MatchTolerance>20</MatchTolerance> | 415 <MatchTolerance>20</MatchTolerance> |
| 383 <MatchToleranceInPpm>True</MatchToleranceInPpm> | 416 <MatchToleranceInPpm>True</MatchToleranceInPpm> |
| 384 <DeisotopeTolerance>7</DeisotopeTolerance> | 417 <DeisotopeTolerance>7</DeisotopeTolerance> |
| 385 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> | 418 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> |
| 386 <DeNovoTolerance>10</DeNovoTolerance> | 419 <DeNovoTolerance>25</DeNovoTolerance> |
| 387 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> | 420 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> |
| 388 <Deisotope>True</Deisotope> | 421 <Deisotope>True</Deisotope> |
| 389 <Topx>12</Topx> | 422 <Topx>12</Topx> |
| 390 <TopxInterval>100</TopxInterval> | 423 <TopxInterval>100</TopxInterval> |
| 391 <HigherCharges>True</HigherCharges> | 424 <HigherCharges>True</HigherCharges> |