Mercurial > repos > galaxyp > maxquant

comparison test-data/07/mqpar.xml @ 21:8934bc76bb52 draft

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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
comparison
equal deleted inserted replaced
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>
344 <timsRemovePrecursor>True</timsRemovePrecursor> 363 <timsRemovePrecursor>True</timsRemovePrecursor>
345 <timsIsobaricLabels>False</timsIsobaricLabels> 364 <timsIsobaricLabels>False</timsIsobaricLabels>
346 <timsCollapseMsms>True</timsCollapseMsms> 365 <timsCollapseMsms>True</timsCollapseMsms>
347 <crossLinkingType>0</crossLinkingType> 366 <crossLinkingType>0</crossLinkingType>
348 <crossLinker/> 367 <crossLinker/>
349 <minMatchXl>0</minMatchXl> 368 <minMatchXl>3</minMatchXl>
350 <minPairedPepLenXl>6</minPairedPepLenXl> 369 <minPairedPepLenXl>6</minPairedPepLenXl>
370 <minScore_Dipeptide>40</minScore_Dipeptide>
371 <minScore_Monopeptide>0</minScore_Monopeptide>
372 <minScore_PartialCross>10</minScore_PartialCross>
351 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 373 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
374 <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
375 <isHybridPrecDetermination>False</isHybridPrecDetermination>
376 <topXcross>3</topXcross>
377 <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
352 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 378 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
353 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> 379 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
354 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> 380 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
355 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> 381 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
356 <crosslinkModifications> 382 <crosslinkModifications>
363 </crosslinkNetworkFiles> 389 </crosslinkNetworkFiles>
364 <crosslinkMode/> 390 <crosslinkMode/>
365 <peakRefinement>False</peakRefinement> 391 <peakRefinement>False</peakRefinement>
366 <isobaricSumOverWindow>True</isobaricSumOverWindow> 392 <isobaricSumOverWindow>True</isobaricSumOverWindow>
367 <isobaricWeightExponent>0.75</isobaricWeightExponent> 393 <isobaricWeightExponent>0.75</isobaricWeightExponent>
394 <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
368 <diaLibraryType>0</diaLibraryType> 395 <diaLibraryType>0</diaLibraryType>
369 <diaLibraryPaths> 396 <diaLibraryPaths>
370 </diaLibraryPaths> 397 </diaLibraryPaths>
371 <diaPeptidePaths> 398 <diaPeptidePaths>
372 </diaPeptidePaths> 399 </diaPeptidePaths>
409 <diaPermuteCcs>False</diaPermuteCcs> 436 <diaPermuteCcs>False</diaPermuteCcs>
410 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> 437 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
411 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> 438 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
412 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> 439 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
413 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> 440 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
441 <diaTransferQvalue>0.3</diaTransferQvalue>
442 <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
443 <diaMinPeaksForRecal>5</diaMinPeaksForRecal>
444 <diaUseFragIntensForMl>False</diaUseFragIntensForMl>
445 <diaUseFragMassesForMl>False</diaUseFragMassesForMl>
446 <diaMaxTrainInstances>1000000</diaMaxTrainInstances>
414 </parameterGroup> 447 </parameterGroup>
415 </parameterGroups> 448 </parameterGroups>
416 <msmsParamsArray> 449 <msmsParamsArray>
417 <msmsParams> 450 <msmsParams>
418 <Name>FTMS</Name> 451 <Name>FTMS</Name>
419 <MatchTolerance>20</MatchTolerance> 452 <MatchTolerance>20</MatchTolerance>
420 <MatchToleranceInPpm>True</MatchToleranceInPpm> 453 <MatchToleranceInPpm>True</MatchToleranceInPpm>
421 <DeisotopeTolerance>7</DeisotopeTolerance> 454 <DeisotopeTolerance>7</DeisotopeTolerance>
422 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> 455 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
423 <DeNovoTolerance>10</DeNovoTolerance> 456 <DeNovoTolerance>25</DeNovoTolerance>
424 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> 457 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
425 <Deisotope>True</Deisotope> 458 <Deisotope>True</Deisotope>
426 <Topx>12</Topx> 459 <Topx>12</Topx>
427 <TopxInterval>100</TopxInterval> 460 <TopxInterval>100</TopxInterval>
428 <HigherCharges>True</HigherCharges> 461 <HigherCharges>True</HigherCharges>
435 <Name>ITMS</Name> 468 <Name>ITMS</Name>
436 <MatchTolerance>0.5</MatchTolerance> 469 <MatchTolerance>0.5</MatchTolerance>
437 <MatchToleranceInPpm>False</MatchToleranceInPpm> 470 <MatchToleranceInPpm>False</MatchToleranceInPpm>
438 <DeisotopeTolerance>0.15</DeisotopeTolerance> 471 <DeisotopeTolerance>0.15</DeisotopeTolerance>
439 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 472 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
440 <DeNovoTolerance>0.25</DeNovoTolerance> 473 <DeNovoTolerance>0.5</DeNovoTolerance>
441 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 474 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
442 <Deisotope>False</Deisotope> 475 <Deisotope>False</Deisotope>
443 <Topx>8</Topx> 476 <Topx>8</Topx>
444 <TopxInterval>100</TopxInterval> 477 <TopxInterval>100</TopxInterval>
445 <HigherCharges>True</HigherCharges> 478 <HigherCharges>True</HigherCharges>
452 <Name>TOF</Name> 485 <Name>TOF</Name>
453 <MatchTolerance>40</MatchTolerance> 486 <MatchTolerance>40</MatchTolerance>
454 <MatchToleranceInPpm>True</MatchToleranceInPpm> 487 <MatchToleranceInPpm>True</MatchToleranceInPpm>
455 <DeisotopeTolerance>0.01</DeisotopeTolerance> 488 <DeisotopeTolerance>0.01</DeisotopeTolerance>
456 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 489 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
457 <DeNovoTolerance>0.02</DeNovoTolerance> 490 <DeNovoTolerance>25</DeNovoTolerance>
458 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 491 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
459 <Deisotope>True</Deisotope> 492 <Deisotope>True</Deisotope>
460 <Topx>10</Topx> 493 <Topx>10</Topx>
461 <TopxInterval>100</TopxInterval> 494 <TopxInterval>100</TopxInterval>
462 <HigherCharges>True</HigherCharges> 495 <HigherCharges>True</HigherCharges>
463 <IncludeWater>True</IncludeWater> 496 <IncludeWater>True</IncludeWater>
469 <Name>Unknown</Name> 502 <Name>Unknown</Name>
470 <MatchTolerance>20</MatchTolerance> 503 <MatchTolerance>20</MatchTolerance>
471 <MatchToleranceInPpm>True</MatchToleranceInPpm> 504 <MatchToleranceInPpm>True</MatchToleranceInPpm>
472 <DeisotopeTolerance>7</DeisotopeTolerance> 505 <DeisotopeTolerance>7</DeisotopeTolerance>
473 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> 506 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
474 <DeNovoTolerance>10</DeNovoTolerance> 507 <DeNovoTolerance>25</DeNovoTolerance>
475 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> 508 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
476 <Deisotope>True</Deisotope> 509 <Deisotope>True</Deisotope>
477 <Topx>12</Topx> 510 <Topx>12</Topx>
478 <TopxInterval>100</TopxInterval> 511 <TopxInterval>100</TopxInterval>
479 <HigherCharges>True</HigherCharges> 512 <HigherCharges>True</HigherCharges>