Mercurial > repos > galaxyp > maxquant

comparison test-data/template.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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children dcd39bcc7481
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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></fastaFilePath>
6 <identifierParseRule>>(.*)</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 <string>Acetyl (Protein N-term)</string>
89 </restrictMods>
90 <matchingTimeWindow>0</matchingTimeWindow>
91 <alignmentTimeWindow>0</alignmentTimeWindow>
92 <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms>
93 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
94 <compositionPrediction>0</compositionPrediction>
95 <quantMode>1</quantMode>
96 <massDifferenceMods>
97 </massDifferenceMods>
98 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
99 <writeMsScansTable>False</writeMsScansTable>
100 <writeMsmsScansTable>True</writeMsmsScansTable>
101 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
102 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
103 <writeMs3ScansTable>True</writeMs3ScansTable>
104 <writeAllPeptidesTable>True</writeAllPeptidesTable>
105 <writeMzRangeTable>True</writeMzRangeTable>
106 <writeMzTab>False</writeMzTab>
107 <disableMd5>False</disableMd5>
108 <cacheBinInds>True</cacheBinInds>
109 <etdIncludeB>False</etdIncludeB>
110 <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets>
111 <stackPeaks>False</stackPeaks>
112 <ms2PrecursorShift>0</ms2PrecursorShift>
113 <complementaryIonPpm>20</complementaryIonPpm>
114 <variationParseRule></variationParseRule>
115 <variationMode>none</variationMode>
116 <useSeriesReporters>False</useSeriesReporters>
117 <name>templateSession</name>
118 <maxQuantVersion>1.6.3.4</maxQuantVersion>
119 <tempFolder></tempFolder>
120 <pluginFolder></pluginFolder>
121 <numThreads>1</numThreads>
122 <emailAddress></emailAddress>
123 <smtpHost></smtpHost>
124 <emailFromAddress></emailFromAddress>
125 <fixedCombinedFolder></fixedCombinedFolder>
126 <fullMinMz>-1.79769313486232E+308</fullMinMz>
127 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
128 <sendEmail>False</sendEmail>
129 <ionCountIntensities>False</ionCountIntensities>
130 <verboseColumnHeaders>False</verboseColumnHeaders>
131 <calcPeakProperties>False</calcPeakProperties>
132 <showCentroidMassDifferences>False</showCentroidMassDifferences>
133 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
134 <useDotNetCore>False</useDotNetCore>
135 <filePaths>
136 <string>file.example.RAW</string>
137 </filePaths>
138 <experiments>
139 <string>experiment.example</string>
140 </experiments>
141 <fractions>
142 <short>32767</short>
143 </fractions>
144 <ptms>
145 <boolean>False</boolean>
146 </ptms>
147 <paramGroupIndices>
148 <int>0</int>
149 </paramGroupIndices>
150 <referenceChannel>
151 <string></string>
152 </referenceChannel>
153 <parameterGroups>
154 <parameterGroup>
155 <msInstrument>0</msInstrument>
156 <maxCharge>7</maxCharge>
157 <minPeakLen>2</minPeakLen>
158 <useMs1Centroids>False</useMs1Centroids>
159 <useMs2Centroids>False</useMs2Centroids>
160 <cutPeaks>True</cutPeaks>
161 <gapScans>1</gapScans>
162 <minTime>NaN</minTime>
163 <maxTime>NaN</maxTime>
164 <matchType>MatchFromAndTo</matchType>
165 <intensityDetermination>0</intensityDetermination>
166 <centroidMatchTol>8</centroidMatchTol>
167 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
168 <centroidHalfWidth>35</centroidHalfWidth>
169 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
170 <valleyFactor>1.4</valleyFactor>
171 <isotopeValleyFactor>1.2</isotopeValleyFactor>
172 <advancedPeakSplitting>False</advancedPeakSplitting>
173 <intensityThreshold>0</intensityThreshold>
174 <labelMods>
175 <string></string>
176 </labelMods>
177 <lcmsRunType>Standard</lcmsRunType>
178 <reQuantify>False</reQuantify>
179 <lfqMode>0</lfqMode>
180 <lfqSkipNorm>False</lfqSkipNorm>
181 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
182 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
183 <lfqMaxFeatures>100000</lfqMaxFeatures>
184 <neucodeMaxPpm>0</neucodeMaxPpm>
185 <neucodeResolution>0</neucodeResolution>
186 <neucodeResolutionInMda>False</neucodeResolutionInMda>
187 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
188 <fastLfq>True</fastLfq>
189 <lfqRestrictFeatures>False</lfqRestrictFeatures>
190 <lfqMinRatioCount>2</lfqMinRatioCount>
191 <maxLabeledAa>0</maxLabeledAa>
192 <maxNmods>5</maxNmods>
193 <maxMissedCleavages>2</maxMissedCleavages>
194 <multiplicity>1</multiplicity>
195 <enzymeMode>0</enzymeMode>
196 <complementaryReporterType>0</complementaryReporterType>
197 <reporterNormalization>0</reporterNormalization>
198 <neucodeIntensityMode>0</neucodeIntensityMode>
199 <fixedModifications>
200 <string>Carbamidomethyl (C)</string>
201 </fixedModifications>
202 <enzymes>
203 <string>Trypsin/P</string>
204 </enzymes>
205 <enzymesFirstSearch>
206 </enzymesFirstSearch>
207 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
208 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
209 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
210 <variableModifications>
211 <string>Oxidation (M)</string>
212 <string>Acetyl (Protein N-term)</string>
213 </variableModifications>
214 <useMultiModification>False</useMultiModification>
215 <multiModifications>
216 </multiModifications>
217 <isobaricLabels>
218 </isobaricLabels>
219 <neucodeLabels>
220 </neucodeLabels>
221 <variableModificationsFirstSearch>
222 </variableModificationsFirstSearch>
223 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
224 <additionalVariableModifications>
225 </additionalVariableModifications>
226 <additionalVariableModificationProteins>
227 </additionalVariableModificationProteins>
228 <doMassFiltering>True</doMassFiltering>
229 <firstSearchTol>20</firstSearchTol>
230 <mainSearchTol>4.5</mainSearchTol>
231 <searchTolInPpm>True</searchTolInPpm>
232 <isotopeMatchTol>2</isotopeMatchTol>
233 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
234 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
235 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
236 <checkMassDeficit>True</checkMassDeficit>
237 <recalibrationInPpm>True</recalibrationInPpm>
238 <intensityDependentCalibration>False</intensityDependentCalibration>
239 <minScoreForCalibration>70</minScoreForCalibration>
240 <matchLibraryFile>False</matchLibraryFile>
241 <libraryFile></libraryFile>
242 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
243 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
244 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
245 <reporterMassTolerance>NaN</reporterMassTolerance>
246 <reporterPif>NaN</reporterPif>
247 <filterPif>False</filterPif>
248 <reporterFraction>NaN</reporterFraction>
249 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
250 <timsHalfWidth>0</timsHalfWidth>
251 <timsStep>0</timsStep>
252 <timsResolution>0</timsResolution>
253 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
254 <timsRemovePrecursor>True</timsRemovePrecursor>
255 <timsIsobaricLabels>False</timsIsobaricLabels>
256 <timsCollapseMsms>True</timsCollapseMsms>
257 <crosslinkSearch>False</crosslinkSearch>
258 <crossLinker></crossLinker>
259 <minMatchXl>0</minMatchXl>
260 <minPairedPepLenXl>6</minPairedPepLenXl>
261 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
262 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
263 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
264 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
265 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
266 <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta>
267 <crosslinkCleaveModifications>
268 </crosslinkCleaveModifications>
269 <crosslinkFastaFiles>
270 </crosslinkFastaFiles>
271 <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
272 <peakRefinement>False</peakRefinement>
273 <isobaricSumOverWindow>True</isobaricSumOverWindow>
274 </parameterGroup>
275 </parameterGroups>
276 <msmsParamsArray>
277 <msmsParams>
278 <Name>FTMS</Name>
279 <MatchTolerance>20</MatchTolerance>
280 <MatchToleranceInPpm>True</MatchToleranceInPpm>
281 <DeisotopeTolerance>7</DeisotopeTolerance>
282 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
283 <DeNovoTolerance>10</DeNovoTolerance>
284 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
285 <Deisotope>True</Deisotope>
286 <Topx>12</Topx>
287 <TopxInterval>100</TopxInterval>
288 <HigherCharges>True</HigherCharges>
289 <IncludeWater>True</IncludeWater>
290 <IncludeAmmonia>True</IncludeAmmonia>
291 <DependentLosses>True</DependentLosses>
292 <Recalibration>False</Recalibration>
293 </msmsParams>
294 <msmsParams>
295 <Name>ITMS</Name>
296 <MatchTolerance>0.5</MatchTolerance>
297 <MatchToleranceInPpm>False</MatchToleranceInPpm>
298 <DeisotopeTolerance>0.15</DeisotopeTolerance>
299 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
300 <DeNovoTolerance>0.25</DeNovoTolerance>
301 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
302 <Deisotope>False</Deisotope>
303 <Topx>8</Topx>
304 <TopxInterval>100</TopxInterval>
305 <HigherCharges>True</HigherCharges>
306 <IncludeWater>True</IncludeWater>
307 <IncludeAmmonia>True</IncludeAmmonia>
308 <DependentLosses>True</DependentLosses>
309 <Recalibration>False</Recalibration>
310 </msmsParams>
311 <msmsParams>
312 <Name>TOF</Name>
313 <MatchTolerance>40</MatchTolerance>
314 <MatchToleranceInPpm>True</MatchToleranceInPpm>
315 <DeisotopeTolerance>0.01</DeisotopeTolerance>
316 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
317 <DeNovoTolerance>0.02</DeNovoTolerance>
318 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
319 <Deisotope>True</Deisotope>
320 <Topx>10</Topx>
321 <TopxInterval>100</TopxInterval>
322 <HigherCharges>True</HigherCharges>
323 <IncludeWater>True</IncludeWater>
324 <IncludeAmmonia>True</IncludeAmmonia>
325 <DependentLosses>True</DependentLosses>
326 <Recalibration>False</Recalibration>
327 </msmsParams>
328 <msmsParams>
329 <Name>Unknown</Name>
330 <MatchTolerance>0.5</MatchTolerance>
331 <MatchToleranceInPpm>False</MatchToleranceInPpm>
332 <DeisotopeTolerance>0.15</DeisotopeTolerance>
333 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
334 <DeNovoTolerance>0.25</DeNovoTolerance>
335 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
336 <Deisotope>False</Deisotope>
337 <Topx>8</Topx>
338 <TopxInterval>100</TopxInterval>
339 <HigherCharges>True</HigherCharges>
340 <IncludeWater>True</IncludeWater>
341 <IncludeAmmonia>True</IncludeAmmonia>
342 <DependentLosses>True</DependentLosses>
343 <Recalibration>False</Recalibration>
344 </msmsParams>
345 </msmsParamsArray>
346 <fragmentationParamsArray>
347 <fragmentationParams>
348 <Name>CID</Name>
349 <Connected>False</Connected>
350 <ConnectedScore0>1</ConnectedScore0>
351 <ConnectedScore1>1</ConnectedScore1>
352 <ConnectedScore2>1</ConnectedScore2>
353 <InternalFragments>False</InternalFragments>
354 <InternalFragmentWeight>1</InternalFragmentWeight>
355 <InternalFragmentAas>KRH</InternalFragmentAas>
356 </fragmentationParams>
357 <fragmentationParams>
358 <Name>HCD</Name>
359 <Connected>False</Connected>
360 <ConnectedScore0>1</ConnectedScore0>
361 <ConnectedScore1>1</ConnectedScore1>
362 <ConnectedScore2>1</ConnectedScore2>
363 <InternalFragments>False</InternalFragments>
364 <InternalFragmentWeight>1</InternalFragmentWeight>
365 <InternalFragmentAas>KRH</InternalFragmentAas>
366 </fragmentationParams>
367 <fragmentationParams>
368 <Name>ETD</Name>
369 <Connected>False</Connected>
370 <ConnectedScore0>1</ConnectedScore0>
371 <ConnectedScore1>1</ConnectedScore1>
372 <ConnectedScore2>1</ConnectedScore2>
373 <InternalFragments>False</InternalFragments>
374 <InternalFragmentWeight>1</InternalFragmentWeight>
375 <InternalFragmentAas>KRH</InternalFragmentAas>
376 </fragmentationParams>
377 <fragmentationParams>
378 <Name>PQD</Name>
379 <Connected>False</Connected>
380 <ConnectedScore0>1</ConnectedScore0>
381 <ConnectedScore1>1</ConnectedScore1>
382 <ConnectedScore2>1</ConnectedScore2>
383 <InternalFragments>False</InternalFragments>
384 <InternalFragmentWeight>1</InternalFragmentWeight>
385 <InternalFragmentAas>KRH</InternalFragmentAas>
386 </fragmentationParams>
387 <fragmentationParams>
388 <Name>ETHCD</Name>
389 <Connected>False</Connected>
390 <ConnectedScore0>1</ConnectedScore0>
391 <ConnectedScore1>1</ConnectedScore1>
392 <ConnectedScore2>1</ConnectedScore2>
393 <InternalFragments>False</InternalFragments>
394 <InternalFragmentWeight>1</InternalFragmentWeight>
395 <InternalFragmentAas>KRH</InternalFragmentAas>
396 </fragmentationParams>
397 <fragmentationParams>
398 <Name>ETCID</Name>
399 <Connected>False</Connected>
400 <ConnectedScore0>1</ConnectedScore0>
401 <ConnectedScore1>1</ConnectedScore1>
402 <ConnectedScore2>1</ConnectedScore2>
403 <InternalFragments>False</InternalFragments>
404 <InternalFragmentWeight>1</InternalFragmentWeight>
405 <InternalFragmentAas>KRH</InternalFragmentAas>
406 </fragmentationParams>
407 <fragmentationParams>
408 <Name>UVPD</Name>
409 <Connected>False</Connected>
410 <ConnectedScore0>1</ConnectedScore0>
411 <ConnectedScore1>1</ConnectedScore1>
412 <ConnectedScore2>1</ConnectedScore2>
413 <InternalFragments>False</InternalFragments>
414 <InternalFragmentWeight>1</InternalFragmentWeight>
415 <InternalFragmentAas>KRH</InternalFragmentAas>
416 </fragmentationParams>
417 <fragmentationParams>
418 <Name>Unknown</Name>
419 <Connected>False</Connected>
420 <ConnectedScore0>1</ConnectedScore0>
421 <ConnectedScore1>1</ConnectedScore1>
422 <ConnectedScore2>1</ConnectedScore2>
423 <InternalFragments>False</InternalFragments>
424 <InternalFragmentWeight>1</InternalFragmentWeight>
425 <InternalFragmentAas>KRH</InternalFragmentAas>
426 </fragmentationParams>
427 </fragmentationParamsArray>
428 </MaxQuantParams>