Mercurial > repos > galaxyp > maxquant

comparison test-data/single/mqpar.xml @ 1:8bac3cc5c5de draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 05:01:05 -0400
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0:d4b6c9eae635 1:8bac3cc5c5de
1 <?xml version="1.0" encoding="utf-8"?>
2 <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>D:\fasta\bsa.fasta</fastaFilePath>
6 <identifierParseRule>>([^\s]*)</identifierParseRule>
7 <descriptionParseRule>>(.*)</descriptionParseRule>
8 <taxonomyParseRule></taxonomyParseRule>
9 <variationParseRule></variationParseRule>
10 <modificationParseRule></modificationParseRule>
11 <taxonomyId></taxonomyId>
12 </FastaFileInfo>
13 </fastaFiles>
14 <fastaFilesProteogenomics>
15 </fastaFilesProteogenomics>
16 <fastaFilesFirstSearch>
17 </fastaFilesFirstSearch>
18 <fixedSearchFolder></fixedSearchFolder>
19 <andromedaCacheSize>350000</andromedaCacheSize>
20 <advancedRatios>True</advancedRatios>
21 <pvalThres>0.005</pvalThres>
22 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
24 <rtShift>False</rtShift>
25 <separateLfq>False</separateLfq>
26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
27 <lfqRequireMsms>True</lfqRequireMsms>
28 <decoyMode>revert</decoyMode>
29 <boxCarMode>all</boxCarMode>
30 <includeContaminants>True</includeContaminants>
31 <maxPeptideMass>4600</maxPeptideMass>
32 <epsilonMutationScore>True</epsilonMutationScore>
33 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
34 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
35 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
36 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
37 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
38 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
39 <secondPeptide>True</secondPeptide>
40 <matchBetweenRuns>False</matchBetweenRuns>
41 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
42 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
43 <dependentPeptides>False</dependentPeptides>
44 <dependentPeptideFdr>0</dependentPeptideFdr>
45 <dependentPeptideMassBin>0</dependentPeptideMassBin>
46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
51 <msmsConnection>False</msmsConnection>
52 <ibaq>False</ibaq>
53 <top3>False</top3>
54 <independentEnzymes>False</independentEnzymes>
55 <useDeltaScore>False</useDeltaScore>
56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
57 <taxonomyLevel>Species</taxonomyLevel>
58 <avalon>False</avalon>
59 <nModColumns>3</nModColumns>
60 <ibaqLogFit>False</ibaqLogFit>
61 <razorProteinFdr>True</razorProteinFdr>
62 <deNovoSequencing>False</deNovoSequencing>
63 <deNovoVarMods>True</deNovoVarMods>
64 <massDifferenceSearch>False</massDifferenceSearch>
65 <isotopeCalc>False</isotopeCalc>
66 <writePeptidesForSpectrumFile></writePeptidesForSpectrumFile>
67 <intensityPredictionsFile>
68 </intensityPredictionsFile>
69 <minPepLen>7</minPepLen>
70 <psmFdrCrosslink>0.01</psmFdrCrosslink>
71 <peptideFdr>0.01</peptideFdr>
72 <proteinFdr>0.01</proteinFdr>
73 <siteFdr>0.01</siteFdr>
74 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
75 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
77 <minPeptides>1</minPeptides>
78 <minRazorPeptides>1</minRazorPeptides>
79 <minUniquePeptides>0</minUniquePeptides>
80 <useCounterparts>False</useCounterparts>
81 <advancedSiteIntensities>True</advancedSiteIntensities>
82 <customProteinQuantification>False</customProteinQuantification>
83 <customProteinQuantificationFile></customProteinQuantificationFile>
84 <minRatioCount>2</minRatioCount>
85 <restrictProteinQuantification>True</restrictProteinQuantification>
86 <restrictMods>
87 <string>Oxidation (M)</string>
88 </restrictMods>
89 <matchingTimeWindow>0</matchingTimeWindow>
90 <alignmentTimeWindow>0</alignmentTimeWindow>
91 <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms>
92 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
93 <compositionPrediction>0</compositionPrediction>
94 <quantMode>1</quantMode>
95 <massDifferenceMods>
96 </massDifferenceMods>
97 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
98 <writeMsScansTable>False</writeMsScansTable>
99 <writeMsmsScansTable>True</writeMsmsScansTable>
100 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
101 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
102 <writeMs3ScansTable>True</writeMs3ScansTable>
103 <writeAllPeptidesTable>True</writeAllPeptidesTable>
104 <writeMzRangeTable>True</writeMzRangeTable>
105 <writeMzTab>True</writeMzTab>
106 <disableMd5>False</disableMd5>
107 <cacheBinInds>True</cacheBinInds>
108 <etdIncludeB>False</etdIncludeB>
109 <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets>
110 <stackPeaks>False</stackPeaks>
111 <ms2PrecursorShift>0</ms2PrecursorShift>
112 <complementaryIonPpm>20</complementaryIonPpm>
113 <variationParseRule></variationParseRule>
114 <variationMode>none</variationMode>
115 <useSeriesReporters>False</useSeriesReporters>
116 <name>session1</name>
117 <maxQuantVersion>1.6.3.4</maxQuantVersion>
118 <tempFolder></tempFolder>
119 <pluginFolder></pluginFolder>
120 <numThreads>1</numThreads>
121 <emailAddress></emailAddress>
122 <smtpHost></smtpHost>
123 <emailFromAddress></emailFromAddress>
124 <fixedCombinedFolder></fixedCombinedFolder>
125 <fullMinMz>-1.79589544172745E+308</fullMinMz>
126 <fullMaxMz>1.79589544172745E+308</fullMaxMz>
127 <sendEmail>False</sendEmail>
128 <ionCountIntensities>False</ionCountIntensities>
129 <verboseColumnHeaders>False</verboseColumnHeaders>
130 <calcPeakProperties>False</calcPeakProperties>
131 <showCentroidMassDifferences>False</showCentroidMassDifferences>
132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
133 <useDotNetCore>False</useDotNetCore>
134 <filePaths>
135 <string>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string>
136 </filePaths>
137 <experiments>
138 <string>BSA_min_23.mzXML</string>
139 </experiments>
140 <fractions>
141 <short>32767</short>
142 </fractions>
143 <ptms>
144 <boolean>False</boolean>
145 </ptms>
146 <paramGroupIndices>
147 <int>0</int>
148 </paramGroupIndices>
149 <referenceChannel>
150 <string></string>
151 </referenceChannel>
152 <parameterGroups>
153 <parameterGroup>
154 <msInstrument>0</msInstrument>
155 <maxCharge>7</maxCharge>
156 <minPeakLen>2</minPeakLen>
157 <useMs1Centroids>False</useMs1Centroids>
158 <useMs2Centroids>False</useMs2Centroids>
159 <cutPeaks>True</cutPeaks>
160 <gapScans>1</gapScans>
161 <minTime>NaN</minTime>
162 <maxTime>NaN</maxTime>
163 <matchType>MatchFromAndTo</matchType>
164 <intensityDetermination>0</intensityDetermination>
165 <centroidMatchTol>8</centroidMatchTol>
166 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
167 <centroidHalfWidth>35</centroidHalfWidth>
168 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
169 <valleyFactor>1.4</valleyFactor>
170 <isotopeValleyFactor>1.2</isotopeValleyFactor>
171 <advancedPeakSplitting>False</advancedPeakSplitting>
172 <intensityThreshold>0</intensityThreshold>
173 <labelMods>
174 <string></string>
175 </labelMods>
176 <lcmsRunType>Standard</lcmsRunType>
177 <reQuantify>False</reQuantify>
178 <lfqMode>0</lfqMode>
179 <lfqSkipNorm>False</lfqSkipNorm>
180 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
181 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
182 <lfqMaxFeatures>100000</lfqMaxFeatures>
183 <neucodeMaxPpm>0</neucodeMaxPpm>
184 <neucodeResolution>0</neucodeResolution>
185 <neucodeResolutionInMda>False</neucodeResolutionInMda>
186 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
187 <fastLfq>True</fastLfq>
188 <lfqRestrictFeatures>False</lfqRestrictFeatures>
189 <lfqMinRatioCount>2</lfqMinRatioCount>
190 <maxLabeledAa>0</maxLabeledAa>
191 <maxNmods>5</maxNmods>
192 <maxMissedCleavages>1</maxMissedCleavages>
193 <multiplicity>1</multiplicity>
194 <enzymeMode>0</enzymeMode>
195 <complementaryReporterType>0</complementaryReporterType>
196 <reporterNormalization>0</reporterNormalization>
197 <neucodeIntensityMode>0</neucodeIntensityMode>
198 <fixedModifications>
199 <string>Carbamidomethyl (C)</string>
200 </fixedModifications>
201 <enzymes>
202 <string>Trypsin/P</string>
203 </enzymes>
204 <enzymesFirstSearch>
205 </enzymesFirstSearch>
206 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
207 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
208 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
209 <variableModifications>
210 <string>Oxidation (M)</string>
211 </variableModifications>
212 <useMultiModification>False</useMultiModification>
213 <multiModifications>
214 </multiModifications>
215 <isobaricLabels>
216 </isobaricLabels>
217 <neucodeLabels>
218 </neucodeLabels>
219 <variableModificationsFirstSearch>
220 </variableModificationsFirstSearch>
221 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
222 <additionalVariableModifications>
223 </additionalVariableModifications>
224 <additionalVariableModificationProteins>
225 </additionalVariableModificationProteins>
226 <doMassFiltering>True</doMassFiltering>
227 <firstSearchTol>20</firstSearchTol>
228 <mainSearchTol>4.5</mainSearchTol>
229 <searchTolInPpm>True</searchTolInPpm>
230 <isotopeMatchTol>2</isotopeMatchTol>
231 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
232 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
233 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
234 <checkMassDeficit>True</checkMassDeficit>
235 <recalibrationInPpm>True</recalibrationInPpm>
236 <intensityDependentCalibration>False</intensityDependentCalibration>
237 <minScoreForCalibration>70</minScoreForCalibration>
238 <matchLibraryFile>False</matchLibraryFile>
239 <libraryFile></libraryFile>
240 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
241 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
242 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
243 <reporterMassTolerance>NaN</reporterMassTolerance>
244 <reporterPif>NaN</reporterPif>
245 <filterPif>False</filterPif>
246 <reporterFraction>NaN</reporterFraction>
247 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
248 <timsHalfWidth>0</timsHalfWidth>
249 <timsStep>0</timsStep>
250 <timsResolution>0</timsResolution>
251 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
252 <timsRemovePrecursor>True</timsRemovePrecursor>
253 <timsIsobaricLabels>False</timsIsobaricLabels>
254 <timsCollapseMsms>True</timsCollapseMsms>
255 <crosslinkSearch>False</crosslinkSearch>
256 <crossLinker></crossLinker>
257 <minMatchXl>0</minMatchXl>
258 <minPairedPepLenXl>6</minPairedPepLenXl>
259 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
260 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
261 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
262 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
263 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
264 <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta>
265 <crosslinkCleaveModifications>
266 </crosslinkCleaveModifications>
267 <crosslinkFastaFiles>
268 </crosslinkFastaFiles>
269 <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
270 <peakRefinement>False</peakRefinement>
271 <isobaricSumOverWindow>True</isobaricSumOverWindow>
272 </parameterGroup>
273 </parameterGroups>
274 <msmsParamsArray>
275 <msmsParams>
276 <Name>FTMS</Name>
277 <MatchTolerance>20</MatchTolerance>
278 <MatchToleranceInPpm>True</MatchToleranceInPpm>
279 <DeisotopeTolerance>7</DeisotopeTolerance>
280 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
281 <DeNovoTolerance>10</DeNovoTolerance>
282 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
283 <Deisotope>True</Deisotope>
284 <Topx>12</Topx>
285 <TopxInterval>100</TopxInterval>
286 <HigherCharges>True</HigherCharges>
287 <IncludeWater>True</IncludeWater>
288 <IncludeAmmonia>True</IncludeAmmonia>
289 <DependentLosses>True</DependentLosses>
290 <Recalibration>False</Recalibration>
291 </msmsParams>
292 <msmsParams>
293 <Name>ITMS</Name>
294 <MatchTolerance>0.5</MatchTolerance>
295 <MatchToleranceInPpm>False</MatchToleranceInPpm>
296 <DeisotopeTolerance>0.15</DeisotopeTolerance>
297 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
298 <DeNovoTolerance>0.25</DeNovoTolerance>
299 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
300 <Deisotope>False</Deisotope>
301 <Topx>8</Topx>
302 <TopxInterval>100</TopxInterval>
303 <HigherCharges>True</HigherCharges>
304 <IncludeWater>True</IncludeWater>
305 <IncludeAmmonia>True</IncludeAmmonia>
306 <DependentLosses>True</DependentLosses>
307 <Recalibration>False</Recalibration>
308 </msmsParams>
309 <msmsParams>
310 <Name>TOF</Name>
311 <MatchTolerance>40</MatchTolerance>
312 <MatchToleranceInPpm>True</MatchToleranceInPpm>
313 <DeisotopeTolerance>0.01</DeisotopeTolerance>
314 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
315 <DeNovoTolerance>0.02</DeNovoTolerance>
316 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
317 <Deisotope>True</Deisotope>
318 <Topx>10</Topx>
319 <TopxInterval>100</TopxInterval>
320 <HigherCharges>True</HigherCharges>
321 <IncludeWater>True</IncludeWater>
322 <IncludeAmmonia>True</IncludeAmmonia>
323 <DependentLosses>True</DependentLosses>
324 <Recalibration>False</Recalibration>
325 </msmsParams>
326 <msmsParams>
327 <Name>Unknown</Name>
328 <MatchTolerance>0.5</MatchTolerance>
329 <MatchToleranceInPpm>False</MatchToleranceInPpm>
330 <DeisotopeTolerance>0.15</DeisotopeTolerance>
331 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
332 <DeNovoTolerance>0.25</DeNovoTolerance>
333 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
334 <Deisotope>False</Deisotope>
335 <Topx>8</Topx>
336 <TopxInterval>100</TopxInterval>
337 <HigherCharges>True</HigherCharges>
338 <IncludeWater>True</IncludeWater>
339 <IncludeAmmonia>True</IncludeAmmonia>
340 <DependentLosses>True</DependentLosses>
341 <Recalibration>False</Recalibration>
342 </msmsParams>
343 </msmsParamsArray>
344 <fragmentationParamsArray>
345 <fragmentationParams>
346 <Name>CID</Name>
347 <Connected>False</Connected>
348 <ConnectedScore0>1</ConnectedScore0>
349 <ConnectedScore1>1</ConnectedScore1>
350 <ConnectedScore2>1</ConnectedScore2>
351 <InternalFragments>False</InternalFragments>
352 <InternalFragmentWeight>1</InternalFragmentWeight>
353 <InternalFragmentAas>KRH</InternalFragmentAas>
354 </fragmentationParams>
355 <fragmentationParams>
356 <Name>HCD</Name>
357 <Connected>False</Connected>
358 <ConnectedScore0>1</ConnectedScore0>
359 <ConnectedScore1>1</ConnectedScore1>
360 <ConnectedScore2>1</ConnectedScore2>
361 <InternalFragments>False</InternalFragments>
362 <InternalFragmentWeight>1</InternalFragmentWeight>
363 <InternalFragmentAas>KRH</InternalFragmentAas>
364 </fragmentationParams>
365 <fragmentationParams>
366 <Name>ETD</Name>
367 <Connected>False</Connected>
368 <ConnectedScore0>1</ConnectedScore0>
369 <ConnectedScore1>1</ConnectedScore1>
370 <ConnectedScore2>1</ConnectedScore2>
371 <InternalFragments>False</InternalFragments>
372 <InternalFragmentWeight>1</InternalFragmentWeight>
373 <InternalFragmentAas>KRH</InternalFragmentAas>
374 </fragmentationParams>
375 <fragmentationParams>
376 <Name>PQD</Name>
377 <Connected>False</Connected>
378 <ConnectedScore0>1</ConnectedScore0>
379 <ConnectedScore1>1</ConnectedScore1>
380 <ConnectedScore2>1</ConnectedScore2>
381 <InternalFragments>False</InternalFragments>
382 <InternalFragmentWeight>1</InternalFragmentWeight>
383 <InternalFragmentAas>KRH</InternalFragmentAas>
384 </fragmentationParams>
385 <fragmentationParams>
386 <Name>ETHCD</Name>
387 <Connected>False</Connected>
388 <ConnectedScore0>1</ConnectedScore0>
389 <ConnectedScore1>1</ConnectedScore1>
390 <ConnectedScore2>1</ConnectedScore2>
391 <InternalFragments>False</InternalFragments>
392 <InternalFragmentWeight>1</InternalFragmentWeight>
393 <InternalFragmentAas>KRH</InternalFragmentAas>
394 </fragmentationParams>
395 <fragmentationParams>
396 <Name>ETCID</Name>
397 <Connected>False</Connected>
398 <ConnectedScore0>1</ConnectedScore0>
399 <ConnectedScore1>1</ConnectedScore1>
400 <ConnectedScore2>1</ConnectedScore2>
401 <InternalFragments>False</InternalFragments>
402 <InternalFragmentWeight>1</InternalFragmentWeight>
403 <InternalFragmentAas>KRH</InternalFragmentAas>
404 </fragmentationParams>
405 <fragmentationParams>
406 <Name>UVPD</Name>
407 <Connected>False</Connected>
408 <ConnectedScore0>1</ConnectedScore0>
409 <ConnectedScore1>1</ConnectedScore1>
410 <ConnectedScore2>1</ConnectedScore2>
411 <InternalFragments>False</InternalFragments>
412 <InternalFragmentWeight>1</InternalFragmentWeight>
413 <InternalFragmentAas>KRH</InternalFragmentAas>
414 </fragmentationParams>
415 <fragmentationParams>
416 <Name>Unknown</Name>
417 <Connected>False</Connected>
418 <ConnectedScore0>1</ConnectedScore0>
419 <ConnectedScore1>1</ConnectedScore1>
420 <ConnectedScore2>1</ConnectedScore2>
421 <InternalFragments>False</InternalFragments>
422 <InternalFragmentWeight>1</InternalFragmentWeight>
423 <InternalFragmentAas>KRH</InternalFragmentAas>
424 </fragmentationParams>
425 </fragmentationParamsArray>
426 </MaxQuantParams>