Mercurial > repos > galaxyp > maxquant

comparison test-data/03/mqpar.xml @ 20:5d013f405259 draft default tip

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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 17:01:43 +0000
parents ef25c9c04aee
children
comparison
equal deleted inserted replaced
19:ef25c9c04aee 20:5d013f405259
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>
296 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> 323 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
297 <diaXgBoostSubSample>0.9</diaXgBoostSubSample> 324 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
298 <centroidPosition>0</centroidPosition> 325 <centroidPosition>0</centroidPosition>
299 <diaQuantMethod>7</diaQuantMethod> 326 <diaQuantMethod>7</diaQuantMethod>
300 <diaFeatureQuantMethod>2</diaFeatureQuantMethod> 327 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
301 <lfqNormType>0</lfqNormType> 328 <lfqNormType>1</lfqNormType>
302 <diaTopNForQuant>10</diaTopNForQuant> 329 <diaTopNForQuant>10</diaTopNForQuant>
303 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> 330 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
304 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> 331 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
305 <diaPrecursorFilterType>0</diaPrecursorFilterType> 332 <diaPrecursorFilterType>0</diaPrecursorFilterType>
306 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> 333 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
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>