Mercurial > repos > galaxyp > maxquant_mqpar

comparison test-data/two/mqpar.xml @ 0:256cc0e17454 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 04:53:23 -0400
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-1:000000000000 0:256cc0e17454
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>False</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>2</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\test2\two_mzxml_short\BSA_min_21.mzXML</string>
136 <string>D:\shared\dglaetzer\maxquant_tool\test2\two_mzxml_short\BSA_min_22.mzXML</string>
137 </filePaths>
138 <experiments>
139 <string>BSA_min_21.mzXML</string>
140 <string>BSA_min_22.mzXML</string>
141 </experiments>
142 <fractions>
143 <short>1</short>
144 <short>2</short>
145 </fractions>
146 <ptms>
147 <boolean>False</boolean>
148 <boolean>False</boolean>
149 </ptms>
150 <paramGroupIndices>
151 <int>0</int>
152 <int>0</int>
153 </paramGroupIndices>
154 <referenceChannel>
155 <string></string>
156 <string></string>
157 </referenceChannel>
158 <parameterGroups>
159 <parameterGroup>
160 <msInstrument>0</msInstrument>
161 <maxCharge>7</maxCharge>
162 <minPeakLen>2</minPeakLen>
163 <useMs1Centroids>False</useMs1Centroids>
164 <useMs2Centroids>False</useMs2Centroids>
165 <cutPeaks>True</cutPeaks>
166 <gapScans>1</gapScans>
167 <minTime>NaN</minTime>
168 <maxTime>NaN</maxTime>
169 <matchType>NoMatching</matchType>
170 <intensityDetermination>0</intensityDetermination>
171 <centroidMatchTol>8</centroidMatchTol>
172 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
173 <centroidHalfWidth>35</centroidHalfWidth>
174 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
175 <valleyFactor>1.4</valleyFactor>
176 <isotopeValleyFactor>1.2</isotopeValleyFactor>
177 <advancedPeakSplitting>False</advancedPeakSplitting>
178 <intensityThreshold>0</intensityThreshold>
179 <labelMods>
180 <string></string>
181 </labelMods>
182 <lcmsRunType>Standard</lcmsRunType>
183 <reQuantify>False</reQuantify>
184 <lfqMode>0</lfqMode>
185 <lfqSkipNorm>False</lfqSkipNorm>
186 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
187 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
188 <lfqMaxFeatures>100000</lfqMaxFeatures>
189 <neucodeMaxPpm>0</neucodeMaxPpm>
190 <neucodeResolution>0</neucodeResolution>
191 <neucodeResolutionInMda>False</neucodeResolutionInMda>
192 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
193 <fastLfq>True</fastLfq>
194 <lfqRestrictFeatures>False</lfqRestrictFeatures>
195 <lfqMinRatioCount>2</lfqMinRatioCount>
196 <maxLabeledAa>0</maxLabeledAa>
197 <maxNmods>2</maxNmods>
198 <maxMissedCleavages>0</maxMissedCleavages>
199 <multiplicity>1</multiplicity>
200 <enzymeMode>0</enzymeMode>
201 <complementaryReporterType>0</complementaryReporterType>
202 <reporterNormalization>0</reporterNormalization>
203 <neucodeIntensityMode>0</neucodeIntensityMode>
204 <fixedModifications>
205 <string>Carbamidomethyl (C)</string>
206 </fixedModifications>
207 <enzymes>
208 <string>Trypsin/P</string>
209 </enzymes>
210 <enzymesFirstSearch>
211 </enzymesFirstSearch>
212 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
213 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
214 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
215 <variableModifications>
216 <string>Oxidation (M)</string>
217 </variableModifications>
218 <useMultiModification>False</useMultiModification>
219 <multiModifications>
220 </multiModifications>
221 <isobaricLabels>
222 </isobaricLabels>
223 <neucodeLabels>
224 </neucodeLabels>
225 <variableModificationsFirstSearch>
226 </variableModificationsFirstSearch>
227 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
228 <additionalVariableModifications>
229 </additionalVariableModifications>
230 <additionalVariableModificationProteins>
231 </additionalVariableModificationProteins>
232 <doMassFiltering>True</doMassFiltering>
233 <firstSearchTol>20</firstSearchTol>
234 <mainSearchTol>4.5</mainSearchTol>
235 <searchTolInPpm>True</searchTolInPpm>
236 <isotopeMatchTol>2</isotopeMatchTol>
237 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
238 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
239 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
240 <checkMassDeficit>True</checkMassDeficit>
241 <recalibrationInPpm>True</recalibrationInPpm>
242 <intensityDependentCalibration>False</intensityDependentCalibration>
243 <minScoreForCalibration>70</minScoreForCalibration>
244 <matchLibraryFile>False</matchLibraryFile>
245 <libraryFile></libraryFile>
246 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
247 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
248 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
249 <reporterMassTolerance>NaN</reporterMassTolerance>
250 <reporterPif>NaN</reporterPif>
251 <filterPif>False</filterPif>
252 <reporterFraction>NaN</reporterFraction>
253 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
254 <timsHalfWidth>0</timsHalfWidth>
255 <timsStep>0</timsStep>
256 <timsResolution>0</timsResolution>
257 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
258 <timsRemovePrecursor>True</timsRemovePrecursor>
259 <timsIsobaricLabels>False</timsIsobaricLabels>
260 <timsCollapseMsms>True</timsCollapseMsms>
261 <crosslinkSearch>False</crosslinkSearch>
262 <crossLinker></crossLinker>
263 <minMatchXl>0</minMatchXl>
264 <minPairedPepLenXl>6</minPairedPepLenXl>
265 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
266 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
267 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
268 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
269 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
270 <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta>
271 <crosslinkCleaveModifications>
272 </crosslinkCleaveModifications>
273 <crosslinkFastaFiles>
274 </crosslinkFastaFiles>
275 <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
276 <peakRefinement>False</peakRefinement>
277 <isobaricSumOverWindow>True</isobaricSumOverWindow>
278 </parameterGroup>
279 </parameterGroups>
280 <msmsParamsArray>
281 <msmsParams>
282 <Name>FTMS</Name>
283 <MatchTolerance>20</MatchTolerance>
284 <MatchToleranceInPpm>True</MatchToleranceInPpm>
285 <DeisotopeTolerance>7</DeisotopeTolerance>
286 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
287 <DeNovoTolerance>10</DeNovoTolerance>
288 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
289 <Deisotope>True</Deisotope>
290 <Topx>12</Topx>
291 <TopxInterval>100</TopxInterval>
292 <HigherCharges>True</HigherCharges>
293 <IncludeWater>True</IncludeWater>
294 <IncludeAmmonia>True</IncludeAmmonia>
295 <DependentLosses>True</DependentLosses>
296 <Recalibration>False</Recalibration>
297 </msmsParams>
298 <msmsParams>
299 <Name>ITMS</Name>
300 <MatchTolerance>0.5</MatchTolerance>
301 <MatchToleranceInPpm>False</MatchToleranceInPpm>
302 <DeisotopeTolerance>0.15</DeisotopeTolerance>
303 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
304 <DeNovoTolerance>0.25</DeNovoTolerance>
305 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
306 <Deisotope>False</Deisotope>
307 <Topx>8</Topx>
308 <TopxInterval>100</TopxInterval>
309 <HigherCharges>True</HigherCharges>
310 <IncludeWater>True</IncludeWater>
311 <IncludeAmmonia>True</IncludeAmmonia>
312 <DependentLosses>True</DependentLosses>
313 <Recalibration>False</Recalibration>
314 </msmsParams>
315 <msmsParams>
316 <Name>TOF</Name>
317 <MatchTolerance>40</MatchTolerance>
318 <MatchToleranceInPpm>True</MatchToleranceInPpm>
319 <DeisotopeTolerance>0.01</DeisotopeTolerance>
320 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
321 <DeNovoTolerance>0.02</DeNovoTolerance>
322 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
323 <Deisotope>True</Deisotope>
324 <Topx>10</Topx>
325 <TopxInterval>100</TopxInterval>
326 <HigherCharges>True</HigherCharges>
327 <IncludeWater>True</IncludeWater>
328 <IncludeAmmonia>True</IncludeAmmonia>
329 <DependentLosses>True</DependentLosses>
330 <Recalibration>False</Recalibration>
331 </msmsParams>
332 <msmsParams>
333 <Name>Unknown</Name>
334 <MatchTolerance>0.5</MatchTolerance>
335 <MatchToleranceInPpm>False</MatchToleranceInPpm>
336 <DeisotopeTolerance>0.15</DeisotopeTolerance>
337 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
338 <DeNovoTolerance>0.25</DeNovoTolerance>
339 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
340 <Deisotope>False</Deisotope>
341 <Topx>8</Topx>
342 <TopxInterval>100</TopxInterval>
343 <HigherCharges>True</HigherCharges>
344 <IncludeWater>True</IncludeWater>
345 <IncludeAmmonia>True</IncludeAmmonia>
346 <DependentLosses>True</DependentLosses>
347 <Recalibration>False</Recalibration>
348 </msmsParams>
349 </msmsParamsArray>
350 <fragmentationParamsArray>
351 <fragmentationParams>
352 <Name>CID</Name>
353 <Connected>False</Connected>
354 <ConnectedScore0>1</ConnectedScore0>
355 <ConnectedScore1>1</ConnectedScore1>
356 <ConnectedScore2>1</ConnectedScore2>
357 <InternalFragments>False</InternalFragments>
358 <InternalFragmentWeight>1</InternalFragmentWeight>
359 <InternalFragmentAas>KRH</InternalFragmentAas>
360 </fragmentationParams>
361 <fragmentationParams>
362 <Name>HCD</Name>
363 <Connected>False</Connected>
364 <ConnectedScore0>1</ConnectedScore0>
365 <ConnectedScore1>1</ConnectedScore1>
366 <ConnectedScore2>1</ConnectedScore2>
367 <InternalFragments>False</InternalFragments>
368 <InternalFragmentWeight>1</InternalFragmentWeight>
369 <InternalFragmentAas>KRH</InternalFragmentAas>
370 </fragmentationParams>
371 <fragmentationParams>
372 <Name>ETD</Name>
373 <Connected>False</Connected>
374 <ConnectedScore0>1</ConnectedScore0>
375 <ConnectedScore1>1</ConnectedScore1>
376 <ConnectedScore2>1</ConnectedScore2>
377 <InternalFragments>False</InternalFragments>
378 <InternalFragmentWeight>1</InternalFragmentWeight>
379 <InternalFragmentAas>KRH</InternalFragmentAas>
380 </fragmentationParams>
381 <fragmentationParams>
382 <Name>PQD</Name>
383 <Connected>False</Connected>
384 <ConnectedScore0>1</ConnectedScore0>
385 <ConnectedScore1>1</ConnectedScore1>
386 <ConnectedScore2>1</ConnectedScore2>
387 <InternalFragments>False</InternalFragments>
388 <InternalFragmentWeight>1</InternalFragmentWeight>
389 <InternalFragmentAas>KRH</InternalFragmentAas>
390 </fragmentationParams>
391 <fragmentationParams>
392 <Name>ETHCD</Name>
393 <Connected>False</Connected>
394 <ConnectedScore0>1</ConnectedScore0>
395 <ConnectedScore1>1</ConnectedScore1>
396 <ConnectedScore2>1</ConnectedScore2>
397 <InternalFragments>False</InternalFragments>
398 <InternalFragmentWeight>1</InternalFragmentWeight>
399 <InternalFragmentAas>KRH</InternalFragmentAas>
400 </fragmentationParams>
401 <fragmentationParams>
402 <Name>ETCID</Name>
403 <Connected>False</Connected>
404 <ConnectedScore0>1</ConnectedScore0>
405 <ConnectedScore1>1</ConnectedScore1>
406 <ConnectedScore2>1</ConnectedScore2>
407 <InternalFragments>False</InternalFragments>
408 <InternalFragmentWeight>1</InternalFragmentWeight>
409 <InternalFragmentAas>KRH</InternalFragmentAas>
410 </fragmentationParams>
411 <fragmentationParams>
412 <Name>UVPD</Name>
413 <Connected>False</Connected>
414 <ConnectedScore0>1</ConnectedScore0>
415 <ConnectedScore1>1</ConnectedScore1>
416 <ConnectedScore2>1</ConnectedScore2>
417 <InternalFragments>False</InternalFragments>
418 <InternalFragmentWeight>1</InternalFragmentWeight>
419 <InternalFragmentAas>KRH</InternalFragmentAas>
420 </fragmentationParams>
421 <fragmentationParams>
422 <Name>Unknown</Name>
423 <Connected>False</Connected>
424 <ConnectedScore0>1</ConnectedScore0>
425 <ConnectedScore1>1</ConnectedScore1>
426 <ConnectedScore2>1</ConnectedScore2>
427 <InternalFragments>False</InternalFragments>
428 <InternalFragmentWeight>1</InternalFragmentWeight>
429 <InternalFragmentAas>KRH</InternalFragmentAas>
430 </fragmentationParams>
431 </fragmentationParamsArray>
432 </MaxQuantParams>