Mercurial > repos > galaxyp > maxquant

comparison test-data/02/mqpar.xml @ 6:2133b0be850a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
author galaxyp
date Wed, 06 May 2020 13:35:51 -0400
parents dcd39bcc7481
children d253b379322b
comparison
equal deleted inserted replaced
5:7f432d87c82c 6:2133b0be850a
25 <separateLfq>False</separateLfq> 25 <separateLfq>False</separateLfq>
26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> 26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
27 <lfqRequireMsms>True</lfqRequireMsms> 27 <lfqRequireMsms>True</lfqRequireMsms>
28 <decoyMode>revert</decoyMode> 28 <decoyMode>revert</decoyMode>
29 <boxCarMode>all</boxCarMode> 29 <boxCarMode>all</boxCarMode>
30 <includeContaminants>True</includeContaminants> 30 <includeContaminants>False</includeContaminants>
31 <maxPeptideMass>4600</maxPeptideMass> 31 <maxPeptideMass>4600</maxPeptideMass>
32 <epsilonMutationScore>True</epsilonMutationScore> 32 <epsilonMutationScore>True</epsilonMutationScore>
33 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> 33 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
34 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> 34 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
35 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> 35 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
75 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> 75 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> 76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
77 <minPeptides>1</minPeptides> 77 <minPeptides>1</minPeptides>
78 <minRazorPeptides>1</minRazorPeptides> 78 <minRazorPeptides>1</minRazorPeptides>
79 <minUniquePeptides>0</minUniquePeptides> 79 <minUniquePeptides>0</minUniquePeptides>
80 <useCounterparts>False</useCounterparts> 80 <useCounterparts>True</useCounterparts>
81 <advancedSiteIntensities>True</advancedSiteIntensities> 81 <advancedSiteIntensities>True</advancedSiteIntensities>
82 <customProteinQuantification>False</customProteinQuantification> 82 <customProteinQuantification>False</customProteinQuantification>
83 <customProteinQuantificationFile/> 83 <customProteinQuantificationFile/>
84 <minRatioCount>2</minRatioCount> 84 <minRatioCount>2</minRatioCount>
85 <restrictProteinQuantification>True</restrictProteinQuantification> 85 <restrictProteinQuantification>True</restrictProteinQuantification>
86 <restrictMods> 86 <restrictMods>
87 <string>Oxidation (M)</string> 87 <string>Pro5</string>
88 <string>Acetyl (Protein N-term)</string> 88 <string>Pro6</string>
89 </restrictMods> 89 </restrictMods>
90 <matchingTimeWindow>0</matchingTimeWindow> 90 <matchingTimeWindow>0</matchingTimeWindow>
91 <matchingIonMobilityWindow>0</matchingIonMobilityWindow> 91 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
92 <alignmentTimeWindow>0</alignmentTimeWindow> 92 <alignmentTimeWindow>0</alignmentTimeWindow>
93 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> 93 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
94 <numberOfCandidatesMsms>15</numberOfCandidatesMsms> 94 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
95 <compositionPrediction>0</compositionPrediction> 95 <compositionPrediction>0</compositionPrediction>
96 <quantMode>1</quantMode> 96 <quantMode>0</quantMode>
97 <massDifferenceMods> 97 <massDifferenceMods>
98 </massDifferenceMods> 98 </massDifferenceMods>
99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> 99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
100 <writeMsScansTable>False</writeMsScansTable> 100 <writeMsScansTable>False</writeMsScansTable>
101 <writeMsmsScansTable>True</writeMsmsScansTable> 101 <writeMsmsScansTable>True</writeMsmsScansTable>
265 <libraryFile/> 265 <libraryFile/>
266 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> 266 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
267 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> 267 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
268 <matchLabelTimeTolMin>0</matchLabelTimeTolMin> 268 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
269 <reporterMassTolerance>0.003</reporterMassTolerance> 269 <reporterMassTolerance>0.003</reporterMassTolerance>
270 <reporterPif>0</reporterPif> 270 <reporterPif>0.6</reporterPif>
271 <filterPif>False</filterPif> 271 <filterPif>False</filterPif>
272 <reporterFraction>0</reporterFraction> 272 <reporterFraction>0</reporterFraction>
273 <reporterBasePeakRatio>0</reporterBasePeakRatio> 273 <reporterBasePeakRatio>0</reporterBasePeakRatio>
274 <timsHalfWidth>0</timsHalfWidth> 274 <timsHalfWidth>0</timsHalfWidth>
275 <timsStep>0</timsStep> 275 <timsStep>0</timsStep>
440 <libraryFile/> 440 <libraryFile/>
441 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> 441 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
442 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> 442 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
443 <matchLabelTimeTolMin>0</matchLabelTimeTolMin> 443 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
444 <reporterMassTolerance>0.003</reporterMassTolerance> 444 <reporterMassTolerance>0.003</reporterMassTolerance>
445 <reporterPif>0</reporterPif> 445 <reporterPif>0.8</reporterPif>
446 <filterPif>False</filterPif> 446 <filterPif>True</filterPif>
447 <reporterFraction>0</reporterFraction> 447 <reporterFraction>0</reporterFraction>
448 <reporterBasePeakRatio>0</reporterBasePeakRatio> 448 <reporterBasePeakRatio>0</reporterBasePeakRatio>
449 <timsHalfWidth>0</timsHalfWidth> 449 <timsHalfWidth>0</timsHalfWidth>
450 <timsStep>0</timsStep> 450 <timsStep>0</timsStep>
451 <timsResolution>0</timsResolution> 451 <timsResolution>0</timsResolution>