Mercurial > repos > galaxyp > maxquant

comparison test-data/04/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>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>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>
263 <timsRemovePrecursor>True</timsRemovePrecursor> 282 <timsRemovePrecursor>True</timsRemovePrecursor>
264 <timsIsobaricLabels>False</timsIsobaricLabels> 283 <timsIsobaricLabels>False</timsIsobaricLabels>
265 <timsCollapseMsms>True</timsCollapseMsms> 284 <timsCollapseMsms>True</timsCollapseMsms>
266 <crossLinkingType>0</crossLinkingType> 285 <crossLinkingType>0</crossLinkingType>
267 <crossLinker/> 286 <crossLinker/>
268 <minMatchXl>0</minMatchXl> 287 <minMatchXl>3</minMatchXl>
269 <minPairedPepLenXl>6</minPairedPepLenXl> 288 <minPairedPepLenXl>6</minPairedPepLenXl>
289 <minScore_Dipeptide>40</minScore_Dipeptide>
290 <minScore_Monopeptide>0</minScore_Monopeptide>
291 <minScore_PartialCross>10</minScore_PartialCross>
270 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 292 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
293 <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
294 <isHybridPrecDetermination>False</isHybridPrecDetermination>
295 <topXcross>3</topXcross>
296 <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
271 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 297 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
272 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> 298 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
273 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> 299 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
274 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> 300 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
275 <crosslinkModifications> 301 <crosslinkModifications>
282 </crosslinkNetworkFiles> 308 </crosslinkNetworkFiles>
283 <crosslinkMode/> 309 <crosslinkMode/>
284 <peakRefinement>False</peakRefinement> 310 <peakRefinement>False</peakRefinement>
285 <isobaricSumOverWindow>True</isobaricSumOverWindow> 311 <isobaricSumOverWindow>True</isobaricSumOverWindow>
286 <isobaricWeightExponent>0.75</isobaricWeightExponent> 312 <isobaricWeightExponent>0.75</isobaricWeightExponent>
313 <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
287 <diaLibraryType>0</diaLibraryType> 314 <diaLibraryType>0</diaLibraryType>
288 <diaLibraryPaths> 315 <diaLibraryPaths>
289 </diaLibraryPaths> 316 </diaLibraryPaths>
290 <diaPeptidePaths> 317 <diaPeptidePaths>
291 </diaPeptidePaths> 318 </diaPeptidePaths>
328 <diaPermuteCcs>False</diaPermuteCcs> 355 <diaPermuteCcs>False</diaPermuteCcs>
329 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> 356 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
330 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> 357 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
331 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> 358 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
332 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> 359 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
360 <diaTransferQvalue>0.3</diaTransferQvalue>
361 <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
362 <diaMinPeaksForRecal>5</diaMinPeaksForRecal>
363 <diaUseFragIntensForMl>False</diaUseFragIntensForMl>
364 <diaUseFragMassesForMl>False</diaUseFragMassesForMl>
365 <diaMaxTrainInstances>1000000</diaMaxTrainInstances>
333 </parameterGroup> 366 </parameterGroup>
334 </parameterGroups> 367 </parameterGroups>
335 <msmsParamsArray> 368 <msmsParamsArray>
336 <msmsParams> 369 <msmsParams>
337 <Name>FTMS</Name> 370 <Name>FTMS</Name>
338 <MatchTolerance>20</MatchTolerance> 371 <MatchTolerance>20</MatchTolerance>
339 <MatchToleranceInPpm>True</MatchToleranceInPpm> 372 <MatchToleranceInPpm>True</MatchToleranceInPpm>
340 <DeisotopeTolerance>7</DeisotopeTolerance> 373 <DeisotopeTolerance>7</DeisotopeTolerance>
341 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> 374 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
342 <DeNovoTolerance>10</DeNovoTolerance> 375 <DeNovoTolerance>25</DeNovoTolerance>
343 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> 376 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
344 <Deisotope>True</Deisotope> 377 <Deisotope>True</Deisotope>
345 <Topx>12</Topx> 378 <Topx>12</Topx>
346 <TopxInterval>100</TopxInterval> 379 <TopxInterval>100</TopxInterval>
347 <HigherCharges>True</HigherCharges> 380 <HigherCharges>True</HigherCharges>
354 <Name>ITMS</Name> 387 <Name>ITMS</Name>
355 <MatchTolerance>0.5</MatchTolerance> 388 <MatchTolerance>0.5</MatchTolerance>
356 <MatchToleranceInPpm>False</MatchToleranceInPpm> 389 <MatchToleranceInPpm>False</MatchToleranceInPpm>
357 <DeisotopeTolerance>0.15</DeisotopeTolerance> 390 <DeisotopeTolerance>0.15</DeisotopeTolerance>
358 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 391 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
359 <DeNovoTolerance>0.25</DeNovoTolerance> 392 <DeNovoTolerance>0.5</DeNovoTolerance>
360 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 393 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
361 <Deisotope>False</Deisotope> 394 <Deisotope>False</Deisotope>
362 <Topx>8</Topx> 395 <Topx>8</Topx>
363 <TopxInterval>100</TopxInterval> 396 <TopxInterval>100</TopxInterval>
364 <HigherCharges>True</HigherCharges> 397 <HigherCharges>True</HigherCharges>
371 <Name>TOF</Name> 404 <Name>TOF</Name>
372 <MatchTolerance>40</MatchTolerance> 405 <MatchTolerance>40</MatchTolerance>
373 <MatchToleranceInPpm>True</MatchToleranceInPpm> 406 <MatchToleranceInPpm>True</MatchToleranceInPpm>
374 <DeisotopeTolerance>0.01</DeisotopeTolerance> 407 <DeisotopeTolerance>0.01</DeisotopeTolerance>
375 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 408 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
376 <DeNovoTolerance>0.02</DeNovoTolerance> 409 <DeNovoTolerance>25</DeNovoTolerance>
377 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 410 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
378 <Deisotope>True</Deisotope> 411 <Deisotope>True</Deisotope>
379 <Topx>10</Topx> 412 <Topx>10</Topx>
380 <TopxInterval>100</TopxInterval> 413 <TopxInterval>100</TopxInterval>
381 <HigherCharges>True</HigherCharges> 414 <HigherCharges>True</HigherCharges>
382 <IncludeWater>True</IncludeWater> 415 <IncludeWater>True</IncludeWater>
388 <Name>Unknown</Name> 421 <Name>Unknown</Name>
389 <MatchTolerance>20</MatchTolerance> 422 <MatchTolerance>20</MatchTolerance>
390 <MatchToleranceInPpm>True</MatchToleranceInPpm> 423 <MatchToleranceInPpm>True</MatchToleranceInPpm>
391 <DeisotopeTolerance>7</DeisotopeTolerance> 424 <DeisotopeTolerance>7</DeisotopeTolerance>
392 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> 425 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
393 <DeNovoTolerance>10</DeNovoTolerance> 426 <DeNovoTolerance>25</DeNovoTolerance>
394 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> 427 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
395 <Deisotope>True</Deisotope> 428 <Deisotope>True</Deisotope>
396 <Topx>12</Topx> 429 <Topx>12</Topx>
397 <TopxInterval>100</TopxInterval> 430 <TopxInterval>100</TopxInterval>
398 <HigherCharges>True</HigherCharges> 431 <HigherCharges>True</HigherCharges>