Mercurial > repos > galaxyp > maxquant

comparison test-data/02/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 0839f84def5e
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>randomize</decoyMode> 27 <decoyMode>randomize</decoyMode>
27 <boxCarMode>all</boxCarMode> 28 <boxCarMode>all</boxCarMode>
28 <includeContaminants>False</includeContaminants> 29 <includeContaminants>False</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>True</writeMzTab> 120 <writeMzTab>True</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>1</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>
155 <string/> 169 <string/>
156 </referenceChannel> 170 </referenceChannel>
157 <intensPred>False</intensPred> 171 <intensPred>False</intensPred>
158 <intensPredModelReTrain>False</intensPredModelReTrain> 172 <intensPredModelReTrain>False</intensPredModelReTrain>
159 <lfqTopNPeptides>0</lfqTopNPeptides> 173 <lfqTopNPeptides>0</lfqTopNPeptides>
174 <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq>
175 <diaFragChargesForQuant>1</diaFragChargesForQuant>
176 <timsRearrangeSpectra>False</timsRearrangeSpectra>
177 <gridSpacing>0.5</gridSpacing>
178 <proteinGroupingFile/>
160 <parameterGroups> 179 <parameterGroups>
161 <parameterGroup> 180 <parameterGroup>
162 <msInstrument>0</msInstrument> 181 <msInstrument>0</msInstrument>
163 <maxCharge>7</maxCharge> 182 <maxCharge>7</maxCharge>
164 <minPeakLen>2</minPeakLen> 183 <minPeakLen>2</minPeakLen>
278 <timsRemovePrecursor>True</timsRemovePrecursor> 297 <timsRemovePrecursor>True</timsRemovePrecursor>
279 <timsIsobaricLabels>False</timsIsobaricLabels> 298 <timsIsobaricLabels>False</timsIsobaricLabels>
280 <timsCollapseMsms>True</timsCollapseMsms> 299 <timsCollapseMsms>True</timsCollapseMsms>
281 <crossLinkingType>0</crossLinkingType> 300 <crossLinkingType>0</crossLinkingType>
282 <crossLinker/> 301 <crossLinker/>
283 <minMatchXl>0</minMatchXl> 302 <minMatchXl>3</minMatchXl>
284 <minPairedPepLenXl>6</minPairedPepLenXl> 303 <minPairedPepLenXl>6</minPairedPepLenXl>
304 <minScore_Dipeptide>40</minScore_Dipeptide>
305 <minScore_Monopeptide>0</minScore_Monopeptide>
306 <minScore_PartialCross>10</minScore_PartialCross>
285 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 307 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
308 <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
309 <isHybridPrecDetermination>False</isHybridPrecDetermination>
310 <topXcross>3</topXcross>
311 <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
286 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 312 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
287 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> 313 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
288 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> 314 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
289 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> 315 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
290 <crosslinkModifications> 316 <crosslinkModifications>
297 </crosslinkNetworkFiles> 323 </crosslinkNetworkFiles>
298 <crosslinkMode/> 324 <crosslinkMode/>
299 <peakRefinement>False</peakRefinement> 325 <peakRefinement>False</peakRefinement>
300 <isobaricSumOverWindow>True</isobaricSumOverWindow> 326 <isobaricSumOverWindow>True</isobaricSumOverWindow>
301 <isobaricWeightExponent>0.75</isobaricWeightExponent> 327 <isobaricWeightExponent>0.75</isobaricWeightExponent>
328 <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
302 <diaLibraryType>0</diaLibraryType> 329 <diaLibraryType>0</diaLibraryType>
303 <diaLibraryPaths> 330 <diaLibraryPaths>
304 </diaLibraryPaths> 331 </diaLibraryPaths>
305 <diaPeptidePaths> 332 <diaPeptidePaths>
306 </diaPeptidePaths> 333 </diaPeptidePaths>
343 <diaPermuteCcs>False</diaPermuteCcs> 370 <diaPermuteCcs>False</diaPermuteCcs>
344 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> 371 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
345 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> 372 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
346 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> 373 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
347 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> 374 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
375 <diaTransferQvalue>0.3</diaTransferQvalue>
376 <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
377 <diaMinPeaksForRecal>5</diaMinPeaksForRecal>
378 <diaUseFragIntensForMl>False</diaUseFragIntensForMl>
379 <diaUseFragMassesForMl>False</diaUseFragMassesForMl>
380 <diaMaxTrainInstances>1000000</diaMaxTrainInstances>
348 </parameterGroup> 381 </parameterGroup>
349 <parameterGroup> 382 <parameterGroup>
350 <msInstrument>0</msInstrument> 383 <msInstrument>0</msInstrument>
351 <maxCharge>7</maxCharge> 384 <maxCharge>7</maxCharge>
352 <minPeakLen>2</minPeakLen> 385 <minPeakLen>2</minPeakLen>
480 <timsRemovePrecursor>True</timsRemovePrecursor> 513 <timsRemovePrecursor>True</timsRemovePrecursor>
481 <timsIsobaricLabels>False</timsIsobaricLabels> 514 <timsIsobaricLabels>False</timsIsobaricLabels>
482 <timsCollapseMsms>True</timsCollapseMsms> 515 <timsCollapseMsms>True</timsCollapseMsms>
483 <crossLinkingType>0</crossLinkingType> 516 <crossLinkingType>0</crossLinkingType>
484 <crossLinker/> 517 <crossLinker/>
485 <minMatchXl>0</minMatchXl> 518 <minMatchXl>3</minMatchXl>
486 <minPairedPepLenXl>6</minPairedPepLenXl> 519 <minPairedPepLenXl>6</minPairedPepLenXl>
520 <minScore_Dipeptide>40</minScore_Dipeptide>
521 <minScore_Monopeptide>0</minScore_Monopeptide>
522 <minScore_PartialCross>10</minScore_PartialCross>
487 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 523 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
524 <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
525 <isHybridPrecDetermination>False</isHybridPrecDetermination>
526 <topXcross>3</topXcross>
527 <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
488 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 528 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
489 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> 529 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
490 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> 530 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
491 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> 531 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
492 <crosslinkModifications> 532 <crosslinkModifications>
499 </crosslinkNetworkFiles> 539 </crosslinkNetworkFiles>
500 <crosslinkMode/> 540 <crosslinkMode/>
501 <peakRefinement>False</peakRefinement> 541 <peakRefinement>False</peakRefinement>
502 <isobaricSumOverWindow>True</isobaricSumOverWindow> 542 <isobaricSumOverWindow>True</isobaricSumOverWindow>
503 <isobaricWeightExponent>0.75</isobaricWeightExponent> 543 <isobaricWeightExponent>0.75</isobaricWeightExponent>
544 <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
504 <diaLibraryType>0</diaLibraryType> 545 <diaLibraryType>0</diaLibraryType>
505 <diaLibraryPaths> 546 <diaLibraryPaths>
506 </diaLibraryPaths> 547 </diaLibraryPaths>
507 <diaPeptidePaths> 548 <diaPeptidePaths>
508 </diaPeptidePaths> 549 </diaPeptidePaths>
545 <diaPermuteCcs>False</diaPermuteCcs> 586 <diaPermuteCcs>False</diaPermuteCcs>
546 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> 587 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
547 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> 588 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
548 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> 589 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
549 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> 590 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
591 <diaTransferQvalue>0.3</diaTransferQvalue>
592 <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
593 <diaMinPeaksForRecal>5</diaMinPeaksForRecal>
594 <diaUseFragIntensForMl>False</diaUseFragIntensForMl>
595 <diaUseFragMassesForMl>False</diaUseFragMassesForMl>
596 <diaMaxTrainInstances>1000000</diaMaxTrainInstances>
550 </parameterGroup> 597 </parameterGroup>
551 </parameterGroups> 598 </parameterGroups>
552 <msmsParamsArray> 599 <msmsParamsArray>
553 <msmsParams> 600 <msmsParams>
554 <Name>FTMS</Name> 601 <Name>FTMS</Name>
555 <MatchTolerance>20</MatchTolerance> 602 <MatchTolerance>20</MatchTolerance>
556 <MatchToleranceInPpm>True</MatchToleranceInPpm> 603 <MatchToleranceInPpm>True</MatchToleranceInPpm>
557 <DeisotopeTolerance>7</DeisotopeTolerance> 604 <DeisotopeTolerance>7</DeisotopeTolerance>
558 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> 605 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
559 <DeNovoTolerance>10</DeNovoTolerance> 606 <DeNovoTolerance>25</DeNovoTolerance>
560 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> 607 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
561 <Deisotope>True</Deisotope> 608 <Deisotope>True</Deisotope>
562 <Topx>12</Topx> 609 <Topx>12</Topx>
563 <TopxInterval>100</TopxInterval> 610 <TopxInterval>100</TopxInterval>
564 <HigherCharges>True</HigherCharges> 611 <HigherCharges>True</HigherCharges>
571 <Name>ITMS</Name> 618 <Name>ITMS</Name>
572 <MatchTolerance>0.5</MatchTolerance> 619 <MatchTolerance>0.5</MatchTolerance>
573 <MatchToleranceInPpm>False</MatchToleranceInPpm> 620 <MatchToleranceInPpm>False</MatchToleranceInPpm>
574 <DeisotopeTolerance>0.15</DeisotopeTolerance> 621 <DeisotopeTolerance>0.15</DeisotopeTolerance>
575 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 622 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
576 <DeNovoTolerance>0.25</DeNovoTolerance> 623 <DeNovoTolerance>0.5</DeNovoTolerance>
577 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 624 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
578 <Deisotope>False</Deisotope> 625 <Deisotope>False</Deisotope>
579 <Topx>8</Topx> 626 <Topx>8</Topx>
580 <TopxInterval>100</TopxInterval> 627 <TopxInterval>100</TopxInterval>
581 <HigherCharges>True</HigherCharges> 628 <HigherCharges>True</HigherCharges>
588 <Name>TOF</Name> 635 <Name>TOF</Name>
589 <MatchTolerance>40</MatchTolerance> 636 <MatchTolerance>40</MatchTolerance>
590 <MatchToleranceInPpm>True</MatchToleranceInPpm> 637 <MatchToleranceInPpm>True</MatchToleranceInPpm>
591 <DeisotopeTolerance>0.01</DeisotopeTolerance> 638 <DeisotopeTolerance>0.01</DeisotopeTolerance>
592 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 639 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
593 <DeNovoTolerance>0.02</DeNovoTolerance> 640 <DeNovoTolerance>25</DeNovoTolerance>
594 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 641 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
595 <Deisotope>True</Deisotope> 642 <Deisotope>True</Deisotope>
596 <Topx>10</Topx> 643 <Topx>10</Topx>
597 <TopxInterval>100</TopxInterval> 644 <TopxInterval>100</TopxInterval>
598 <HigherCharges>True</HigherCharges> 645 <HigherCharges>True</HigherCharges>
599 <IncludeWater>True</IncludeWater> 646 <IncludeWater>True</IncludeWater>
605 <Name>Unknown</Name> 652 <Name>Unknown</Name>
606 <MatchTolerance>20</MatchTolerance> 653 <MatchTolerance>20</MatchTolerance>
607 <MatchToleranceInPpm>True</MatchToleranceInPpm> 654 <MatchToleranceInPpm>True</MatchToleranceInPpm>
608 <DeisotopeTolerance>7</DeisotopeTolerance> 655 <DeisotopeTolerance>7</DeisotopeTolerance>
609 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> 656 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
610 <DeNovoTolerance>10</DeNovoTolerance> 657 <DeNovoTolerance>25</DeNovoTolerance>
611 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> 658 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
612 <Deisotope>True</Deisotope> 659 <Deisotope>True</Deisotope>
613 <Topx>12</Topx> 660 <Topx>12</Topx>
614 <TopxInterval>100</TopxInterval> 661 <TopxInterval>100</TopxInterval>
615 <HigherCharges>True</HigherCharges> 662 <HigherCharges>True</HigherCharges>