Mercurial > repos > galaxyp > maxquant

annotate test-data/05/mqpar.xml @ 17:1f39c833f65f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit cda481171e25f6f18c090ae491e9fb68589ffae8
author galaxyp
date Mon, 25 Jul 2022 17:37:01 +0000
parents 181bd6a5f6ce
children 837224ad1694
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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1 <?xml version="1.0" ?>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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2 <MaxQuantParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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3 <fastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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4 <FastaFileInfo>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
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diff changeset
5 <fastaFilePath>/tmp/tmpwu9ns_ue/files/3/1/3/dataset_31390cc5-8f5d-4820-a5e4-e5779aca2b4b.dat</fastaFilePath>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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6 <identifierParseRule>^&gt;.*\|(.*)\|.*$</identifierParseRule>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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7 <descriptionParseRule>^&gt;.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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8 <taxonomyParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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9 <variationParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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10 <modificationParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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11 <taxonomyId/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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12 </FastaFileInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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13 </fastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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14 <fastaFilesProteogenomics>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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15 </fastaFilesProteogenomics>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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16 <fastaFilesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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17 </fastaFilesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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18 <fixedSearchFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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19 <andromedaCacheSize>350000</andromedaCacheSize>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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20 <advancedRatios>True</advancedRatios>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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21 <pvalThres>0.005</pvalThres>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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22 <rtShift>False</rtShift>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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23 <separateLfq>False</separateLfq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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25 <lfqRequireMsms>True</lfqRequireMsms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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26 <decoyMode>revert</decoyMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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27 <boxCarMode>all</boxCarMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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28 <includeContaminants>True</includeContaminants>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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29 <maxPeptideMass>4600</maxPeptideMass>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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30 <epsilonMutationScore>True</epsilonMutationScore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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31 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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32 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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33 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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34 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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35 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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36 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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37 <secondPeptide>True</secondPeptide>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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38 <matchBetweenRuns>True</matchBetweenRuns>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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39 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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40 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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41 <dependentPeptides>False</dependentPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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42 <dependentPeptideFdr>0</dependentPeptideFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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43 <dependentPeptideMassBin>0</dependentPeptideMassBin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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49 <ibaq>True</ibaq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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50 <top3>False</top3>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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51 <independentEnzymes>False</independentEnzymes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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52 <useDeltaScore>False</useDeltaScore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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54 <taxonomyLevel>Species</taxonomyLevel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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55 <avalon>False</avalon>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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56 <nModColumns>3</nModColumns>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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57 <ibaqLogFit>False</ibaqLogFit>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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58 <razorProteinFdr>True</razorProteinFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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59 <deNovoSequencing>False</deNovoSequencing>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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60 <deNovoVarMods>True</deNovoVarMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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61 <massDifferenceSearch>False</massDifferenceSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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62 <isotopeCalc>False</isotopeCalc>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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63 <writePeptidesForSpectrumFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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64 <intensityPredictionsFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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65 </intensityPredictionsFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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66 <minPepLen>7</minPepLen>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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67 <psmFdrCrosslink>0.01</psmFdrCrosslink>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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68 <peptideFdr>0.01</peptideFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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69 <proteinFdr>0.01</proteinFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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70 <siteFdr>0.01</siteFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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71 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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72 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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73 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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74 <minPeptides>1</minPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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75 <minRazorPeptides>1</minRazorPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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76 <minUniquePeptides>1</minUniquePeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
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77 <useCounterparts>True</useCounterparts>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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78 <advancedSiteIntensities>True</advancedSiteIntensities>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
79 <customProteinQuantification>False</customProteinQuantification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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80 <customProteinQuantificationFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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81 <minRatioCount>2</minRatioCount>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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82 <restrictProteinQuantification>True</restrictProteinQuantification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
83 <restrictMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
84 <string>Oxidation (M)</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
85 <string>Acetyl (Protein N-term)</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
86 </restrictMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
87 <matchingTimeWindow>0.7</matchingTimeWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
88 <matchingIonMobilityWindow>0.05</matchingIonMobilityWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
89 <alignmentTimeWindow>20</alignmentTimeWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
90 <alignmentIonMobilityWindow>1</alignmentIonMobilityWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
91 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
92 <compositionPrediction>0</compositionPrediction>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
93 <quantMode>1</quantMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
94 <massDifferenceMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
95 </massDifferenceMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
97 <writeMsScansTable>False</writeMsScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
98 <writeMsmsScansTable>True</writeMsmsScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
101 <writeMs3ScansTable>True</writeMs3ScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
102 <writeAllPeptidesTable>True</writeAllPeptidesTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
103 <writeMzRangeTable>True</writeMzRangeTable>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
105 <writeMzTab>False</writeMzTab>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
106 <disableMd5>False</disableMd5>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
107 <cacheBinInds>True</cacheBinInds>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
108 <etdIncludeB>False</etdIncludeB>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
109 <ms2PrecursorShift>0</ms2PrecursorShift>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
110 <complementaryIonPpm>20</complementaryIonPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
111 <variationParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
112 <variationMode>none</variationMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
113 <useSeriesReporters>False</useSeriesReporters>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
114 <name>templateSession</name>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
115 <maxQuantVersion>1.6.17.0</maxQuantVersion>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
116 <pluginFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
117 <numThreads>1</numThreads>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
118 <batchSize>1</batchSize>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
119 <emailAddress/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
120 <smtpHost/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
121 <emailFromAddress/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
122 <fixedCombinedFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
123 <fullMinMz>-1.79769313486232E+308</fullMinMz>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
124 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
125 <sendEmail>False</sendEmail>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
126 <ionCountIntensities>False</ionCountIntensities>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
127 <verboseColumnHeaders>False</verboseColumnHeaders>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
128 <calcPeakProperties>False</calcPeakProperties>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
129 <showCentroidMassDifferences>False</showCentroidMassDifferences>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
131 <useDotNetCore>True</useDotNetCore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
132 <profilePerformance>False</profilePerformance>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
133 <filePaths>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
134 <string>/tmp/tmpwu9ns_ue/job_working_directory/000/9/working/BSA_min_22.mzxml</string>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
135 </filePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
136 <experiments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
137 <string>BSA_min_22.mzxml</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
138 </experiments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
139 <fractions>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
140 <short>32767</short>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
141 </fractions>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
142 <ptms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
143 <boolean>False</boolean>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
144 </ptms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
145 <paramGroupIndices>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
146 <int>0</int>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
147 </paramGroupIndices>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
148 <referenceChannel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
149 <string/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
150 </referenceChannel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
151 <intensPred>False</intensPred>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
152 <intensPredModelReTrain>False</intensPredModelReTrain>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
153 <lfqTopNPeptides>0</lfqTopNPeptides>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
154 <parameterGroups>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
155 <parameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
156 <msInstrument>0</msInstrument>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
157 <maxCharge>7</maxCharge>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
158 <minPeakLen>2</minPeakLen>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
159 <diaMinPeakLen>1</diaMinPeakLen>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
160 <useMs1Centroids>False</useMs1Centroids>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
161 <useMs2Centroids>False</useMs2Centroids>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
162 <cutPeaks>True</cutPeaks>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
163 <gapScans>1</gapScans>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
164 <minTime>NaN</minTime>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
165 <maxTime>NaN</maxTime>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
166 <matchType>MatchFromAndTo</matchType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
167 <intensityDetermination>0</intensityDetermination>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
168 <centroidMatchTol>8</centroidMatchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
169 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
170 <centroidHalfWidth>35</centroidHalfWidth>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
171 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
172 <valleyFactor>1.4</valleyFactor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
173 <isotopeValleyFactor>1.2</isotopeValleyFactor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
174 <advancedPeakSplitting>False</advancedPeakSplitting>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
175 <intensityThresholdMs1>0</intensityThresholdMs1>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
176 <intensityThresholdMs2>0</intensityThresholdMs2>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
177 <labelMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
178 <string/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
179 </labelMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
180 <lcmsRunType>Standard</lcmsRunType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
181 <reQuantify>False</reQuantify>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
182 <lfqMode>1</lfqMode>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
183 <lfqNormClusterSize>80</lfqNormClusterSize>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
184 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
185 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
186 <lfqMaxFeatures>100000</lfqMaxFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
187 <neucodeMaxPpm>0</neucodeMaxPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
188 <neucodeResolution>0</neucodeResolution>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
189 <neucodeResolutionInMda>False</neucodeResolutionInMda>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
190 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
191 <fastLfq>True</fastLfq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
192 <lfqRestrictFeatures>False</lfqRestrictFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
193 <lfqMinRatioCount>2</lfqMinRatioCount>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
194 <maxLabeledAa>0</maxLabeledAa>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
195 <maxNmods>5</maxNmods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
196 <maxMissedCleavages>1</maxMissedCleavages>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
197 <multiplicity>1</multiplicity>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
198 <enzymeMode>0</enzymeMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
199 <complementaryReporterType>0</complementaryReporterType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
200 <reporterNormalization>0</reporterNormalization>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
201 <neucodeIntensityMode>0</neucodeIntensityMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
202 <fixedModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
203 <string>Carbamidomethyl (C)</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
204 </fixedModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
205 <enzymes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
206 <string>Trypsin/P</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
207 </enzymes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
208 <enzymesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
209 </enzymesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
210 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
211 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
212 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
213 <variableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
214 <string>Oxidation (M)</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
215 </variableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
216 <useMultiModification>False</useMultiModification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
217 <multiModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
218 </multiModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
219 <isobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
220 </isobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
221 <neucodeLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
222 </neucodeLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
223 <variableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
224 </variableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
225 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
226 <additionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
227 </additionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
228 <additionalVariableModificationProteins>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
229 </additionalVariableModificationProteins>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
230 <doMassFiltering>True</doMassFiltering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
231 <firstSearchTol>20</firstSearchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
232 <mainSearchTol>4.5</mainSearchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
233 <searchTolInPpm>True</searchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
234 <isotopeMatchTol>2</isotopeMatchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
235 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
236 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
237 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
238 <checkMassDeficit>True</checkMassDeficit>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
239 <recalibrationInPpm>True</recalibrationInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
240 <intensityDependentCalibration>False</intensityDependentCalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
241 <minScoreForCalibration>70</minScoreForCalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
242 <matchLibraryFile>False</matchLibraryFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
243 <libraryFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
244 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
245 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
246 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
247 <reporterMassTolerance>NaN</reporterMassTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
248 <reporterPif>NaN</reporterPif>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
249 <filterPif>False</filterPif>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
250 <reporterFraction>NaN</reporterFraction>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
251 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
252 <timsHalfWidth>0</timsHalfWidth>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
253 <timsStep>0</timsStep>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
254 <timsResolution>0</timsResolution>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
255 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
256 <timsRemovePrecursor>True</timsRemovePrecursor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
257 <timsIsobaricLabels>False</timsIsobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
258 <timsCollapseMsms>True</timsCollapseMsms>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
259 <crossLinkingType>0</crossLinkingType>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
260 <crossLinker/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
261 <minMatchXl>0</minMatchXl>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
262 <minPairedPepLenXl>6</minPairedPepLenXl>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
263 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
264 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
265 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
266 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
267 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
268 <crosslinkModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
269 </crosslinkModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
270 <crosslinkFastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
271 </crosslinkFastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
272 <crosslinkSites>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
273 </crosslinkSites>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
274 <crosslinkNetworkFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
275 </crosslinkNetworkFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
276 <crosslinkMode/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
277 <peakRefinement>False</peakRefinement>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
278 <isobaricSumOverWindow>True</isobaricSumOverWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
279 <isobaricWeightExponent>0.75</isobaricWeightExponent>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
280 <diaLibraryType>0</diaLibraryType>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
281 <diaLibraryPaths>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
282 </diaLibraryPaths>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
283 <diaPeptidePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
284 </diaPeptidePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
285 <diaEvidencePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
286 </diaEvidencePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
287 <diaMsmsPaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
288 </diaMsmsPaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
289 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
290 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
291 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
292 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
293 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
294 <diaScoreN>7</diaScoreN>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
295 <diaMinScore>1.99</diaMinScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
296 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
297 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
298 <centroidPosition>0</centroidPosition>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
299 <diaQuantMethod>7</diaQuantMethod>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
300 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
13
181bd6a5f6ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ea679515491b0e9e13ec0084b59a40457eb355cc"
galaxyp
parents: 12
diff changeset
301 <lfqNormType>1</lfqNormType>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
302 <diaTopNForQuant>10</diaTopNForQuant>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
303 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
304 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
305 <diaPrecursorFilterType>0</diaPrecursorFilterType>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
306 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
307 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
308 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
309 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
310 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
311 <diaXgBoostEstimators>580</diaXgBoostEstimators>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
312 <diaXgBoostGamma>0.9</diaXgBoostGamma>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
313 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
314 <diaGlobalMl>True</diaGlobalMl>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
315 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
316 <diaMassWindowFactor>3.3</diaMassWindowFactor>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
317 <diaRtPrediction>False</diaRtPrediction>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
318 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
319 <diaNoMl>False</diaNoMl>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
320 <diaPermuteRt>False</diaPermuteRt>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
321 <diaPermuteCcs>False</diaPermuteCcs>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
322 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
323 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
324 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 10
diff changeset
325 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
326 </parameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
327 </parameterGroups>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
328 <msmsParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
329 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
330 <Name>FTMS</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
331 <MatchTolerance>20</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
332 <MatchToleranceInPpm>True</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
333 <DeisotopeTolerance>7</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
334 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
335 <DeNovoTolerance>10</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
336 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
337 <Deisotope>True</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
338 <Topx>12</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
339 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
340 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
341 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
342 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
343 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
344 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
345 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
346 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
347 <Name>ITMS</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
348 <MatchTolerance>0.5</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
349 <MatchToleranceInPpm>False</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
350 <DeisotopeTolerance>0.15</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
351 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
352 <DeNovoTolerance>0.25</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
353 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
354 <Deisotope>False</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
355 <Topx>8</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
356 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
357 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
358 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
359 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
360 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
361 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
362 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
363 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
364 <Name>TOF</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
365 <MatchTolerance>40</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
366 <MatchToleranceInPpm>True</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
367 <DeisotopeTolerance>0.01</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
368 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
369 <DeNovoTolerance>0.02</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
370 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
371 <Deisotope>True</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
372 <Topx>10</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
373 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
374 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
375 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
376 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
377 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
378 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
379 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
380 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
381 <Name>Unknown</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
382 <MatchTolerance>20</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
383 <MatchToleranceInPpm>True</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
384 <DeisotopeTolerance>7</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
385 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
386 <DeNovoTolerance>10</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
387 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
388 <Deisotope>True</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
389 <Topx>12</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
390 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
391 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
392 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
393 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
394 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
395 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
396 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
397 </msmsParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
398 <fragmentationParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
399 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
400 <Name>CID</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
401 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
402 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
403 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
404 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
405 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
406 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
407 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
408 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
409 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
410 <Name>HCD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
411 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
412 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
413 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
414 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
415 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
416 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
417 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
418 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
419 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
420 <Name>ETD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
421 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
422 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
423 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
424 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
425 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
426 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
427 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
428 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
429 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
430 <Name>PQD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
431 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
432 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
433 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
434 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
435 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
436 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
437 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
438 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
439 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
440 <Name>ETHCD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
441 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
442 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
443 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
444 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
445 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
446 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
447 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
448 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
449 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
450 <Name>ETCID</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
451 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
452 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
453 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
454 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
455 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
456 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
457 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
458 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
459 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
460 <Name>UVPD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
461 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
462 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
463 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
464 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
465 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
466 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
467 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
468 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
469 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
470 <Name>Unknown</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
471 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
472 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
473 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
474 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
475 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
476 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
477 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
478 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
479 </fragmentationParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
480 </MaxQuantParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
481