Mercurial > repos > galaxyp > maxquant

comparison test-data/02/mqpar.xml @ 6:f2f79f0be7d1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
author galaxyp
date Mon, 01 Jun 2020 15:50:52 +0000
parents 1cdde5989a2d
children 057bf124c80e
comparison
equal deleted inserted replaced
5:1cdde5989a2d 6:f2f79f0be7d1
23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> 23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
24 <rtShift>False</rtShift> 24 <rtShift>False</rtShift>
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>randomize</decoyMode>
29 <boxCarMode>all</boxCarMode> 29 <boxCarMode>all</boxCarMode>
30 <includeContaminants>False</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>
66 <writePeptidesForSpectrumFile/> 66 <writePeptidesForSpectrumFile/>
67 <intensityPredictionsFile> 67 <intensityPredictionsFile>
68 </intensityPredictionsFile> 68 </intensityPredictionsFile>
69 <minPepLen>7</minPepLen> 69 <minPepLen>7</minPepLen>
70 <psmFdrCrosslink>0.01</psmFdrCrosslink> 70 <psmFdrCrosslink>0.01</psmFdrCrosslink>
71 <peptideFdr>0.01</peptideFdr> 71 <peptideFdr>0.5</peptideFdr>
72 <proteinFdr>0.01</proteinFdr> 72 <proteinFdr>0.4</proteinFdr>
73 <siteFdr>0.01</siteFdr> 73 <siteFdr>0.01</siteFdr>
74 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> 74 <minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>
75 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> 75 <maxPeptideLengthForUnspecificSearch>24</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>True</useCounterparts> 80 <useCounterparts>True</useCounterparts>
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>0.6</reporterPif> 270 <reporterPif>0</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>