Mercurial > repos > galaxyp > maxquant

annotate test-data/04/mqpar.xml @ 21:8934bc76bb52 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
author galaxyp
date Mon, 19 Jun 2023 17:02:17 +0000
parents 0839f84def5e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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1 <?xml version="1.0" ?>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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2 <MaxQuantParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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3 <fastaFiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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4 <FastaFileInfo>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
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5 <fastaFilePath>/tmp/tmpyzym30dx/files/a/5/9/dataset_a592c8b5-872b-4804-9f05-abeef0fda2f1.dat</fastaFilePath>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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7 <descriptionParseRule>&gt;(.*)</descriptionParseRule>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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8 <taxonomyParseRule/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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9 <variationParseRule/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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10 <modificationParseRule/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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11 <taxonomyId/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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12 </FastaFileInfo>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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13 </fastaFiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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14 <fastaFilesProteogenomics>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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15 </fastaFilesProteogenomics>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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16 <fastaFilesFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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17 </fastaFilesFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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18 <fixedSearchFolder/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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19 <andromedaCacheSize>350000</andromedaCacheSize>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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20 <advancedRatios>True</advancedRatios>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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21 <pvalThres>0.005</pvalThres>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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22 <rtShift>False</rtShift>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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23 <separateLfq>False</separateLfq>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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25 <lfqRequireMsms>True</lfqRequireMsms>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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26 <lfqBayesQuant>False</lfqBayesQuant>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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27 <decoyMode>revert</decoyMode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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28 <boxCarMode>all</boxCarMode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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29 <includeContaminants>True</includeContaminants>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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30 <maxPeptideMass>4600</maxPeptideMass>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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31 <epsilonMutationScore>True</epsilonMutationScore>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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32 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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33 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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34 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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35 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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36 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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37 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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38 <secondPeptide>True</secondPeptide>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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39 <matchBetweenRuns>False</matchBetweenRuns>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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40 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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41 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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42 <dependentPeptides>False</dependentPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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43 <dependentPeptideFdr>0</dependentPeptideFdr>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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44 <dependentPeptideMassBin>0</dependentPeptideMassBin>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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45 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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46 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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47 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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48 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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49 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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50 <ibaq>False</ibaq>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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51 <top3>False</top3>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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52 <independentEnzymes>False</independentEnzymes>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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53 <useDeltaScore>False</useDeltaScore>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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54 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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55 <taxonomyLevel>Species</taxonomyLevel>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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56 <avalon>False</avalon>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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57 <nModColumns>3</nModColumns>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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58 <ibaqLogFit>False</ibaqLogFit>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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59 <ibaqChargeNormalization>False</ibaqChargeNormalization>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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60 <razorProteinFdr>True</razorProteinFdr>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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61 <deNovoSequencing>False</deNovoSequencing>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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62 <deNovoVarMods>False</deNovoVarMods>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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63 <deNovoCompleteSequence>False</deNovoCompleteSequence>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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64 <deNovoCalibratedMasses>False</deNovoCalibratedMasses>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
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65 <deNovoMaxIterations>0</deNovoMaxIterations>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
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66 <deNovoProteaseReward>0</deNovoProteaseReward>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
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67 <deNovoProteaseRewardTof>0</deNovoProteaseRewardTof>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
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68 <deNovoAgPenalty>0</deNovoAgPenalty>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
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69 <deNovoGgPenalty>0</deNovoGgPenalty>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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70 <deNovoUseComplementScore>True</deNovoUseComplementScore>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
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71 <deNovoUseProteaseScore>True</deNovoUseProteaseScore>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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72 <deNovoUseWaterLossScore>True</deNovoUseWaterLossScore>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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73 <deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
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74 <deNovoUseA2Score>True</deNovoUseA2Score>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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75 <massDifferenceSearch>False</massDifferenceSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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76 <isotopeCalc>False</isotopeCalc>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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77 <writePeptidesForSpectrumFile/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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78 <intensityPredictionsFile>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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79 </intensityPredictionsFile>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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80 <minPepLen>7</minPepLen>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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81 <psmFdrCrosslink>0.01</psmFdrCrosslink>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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82 <peptideFdr>0.01</peptideFdr>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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83 <proteinFdr>0.01</proteinFdr>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
84 <siteFdr>0.01</siteFdr>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
85 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
86 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
87 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
88 <minPeptides>1</minPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
89 <minRazorPeptides>1</minRazorPeptides>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
90 <minUniquePeptides>0</minUniquePeptides>
6
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 4
diff changeset
91 <useCounterparts>True</useCounterparts>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
92 <advancedSiteIntensities>True</advancedSiteIntensities>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
93 <customProteinQuantification>False</customProteinQuantification>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
94 <customProteinQuantificationFile/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
95 <minRatioCount>2</minRatioCount>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
96 <restrictProteinQuantification>True</restrictProteinQuantification>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
97 <restrictMods>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
98 <string>Oxidation (M)</string>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
99 <string>Acetyl (Protein N-term)</string>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
100 </restrictMods>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
101 <matchingTimeWindow>0</matchingTimeWindow>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
102 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
103 <alignmentTimeWindow>0</alignmentTimeWindow>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
104 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
105 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
106 <compositionPrediction>0</compositionPrediction>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
107 <quantMode>1</quantMode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
108 <massDifferenceMods>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
109 </massDifferenceMods>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
110 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
111 <writeMsScansTable>False</writeMsScansTable>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
112 <writeMsmsScansTable>True</writeMsmsScansTable>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
113 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
114 <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
115 <writeMs3ScansTable>True</writeMs3ScansTable>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
116 <writeAllPeptidesTable>True</writeAllPeptidesTable>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
117 <writeMzRangeTable>True</writeMzRangeTable>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
118 <writeDiaFragmentTable>False</writeDiaFragmentTable>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
119 <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
120 <writeMzTab>False</writeMzTab>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
121 <disableMd5>False</disableMd5>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
122 <cacheBinInds>True</cacheBinInds>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
123 <etdIncludeB>False</etdIncludeB>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
124 <ms2PrecursorShift>0</ms2PrecursorShift>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
125 <complementaryIonPpm>20</complementaryIonPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
126 <variationParseRule/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
127 <variationMode>none</variationMode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
128 <useSeriesReporters>False</useSeriesReporters>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
129 <name>templateSession</name>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
130 <maxQuantVersion>2.0.3.0</maxQuantVersion>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
131 <pluginFolder/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
132 <numThreads>1</numThreads>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
133 <emailAddress/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
134 <smtpHost/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
135 <emailFromAddress/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
136 <fixedCombinedFolder/>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
137 <fullMinMz>-1.79769313486232E+308</fullMinMz>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
138 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
139 <sendEmail>False</sendEmail>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
140 <ionCountIntensities>False</ionCountIntensities>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
141 <verboseColumnHeaders>False</verboseColumnHeaders>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
142 <calcPeakProperties>False</calcPeakProperties>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
143 <showCentroidMassDifferences>False</showCentroidMassDifferences>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
144 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
145 <useDotNetCore>True</useDotNetCore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
146 <profilePerformance>False</profilePerformance>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
147 <filePaths>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
148 <string>/tmp/tmpyzym30dx/job_working_directory/000/22/working/BSA_min_22.mzxml</string>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
149 <string>/tmp/tmpyzym30dx/job_working_directory/000/22/working/BSA_min_23.mzXML</string>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
150 </filePaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
151 <experiments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
152 <string>e1</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
153 <string>e2</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
154 </experiments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
155 <fractions>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
156 <short>1</short>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
157 <short>2</short>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
158 </fractions>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
159 <ptms>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
160 <boolean>False</boolean>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
161 <boolean>False</boolean>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
162 </ptms>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
163 <paramGroupIndices>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
164 <int>0</int>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
165 <int>0</int>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
166 </paramGroupIndices>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
167 <referenceChannel>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
168 <string/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
169 <string/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
170 </referenceChannel>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
171 <intensPred>False</intensPred>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
172 <intensPredModelReTrain>False</intensPredModelReTrain>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
173 <lfqTopNPeptides>0</lfqTopNPeptides>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
174 <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
175 <diaFragChargesForQuant>1</diaFragChargesForQuant>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
176 <timsRearrangeSpectra>False</timsRearrangeSpectra>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
177 <gridSpacing>0.5</gridSpacing>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
178 <proteinGroupingFile/>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
179 <parameterGroups>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
180 <parameterGroup>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
181 <msInstrument>0</msInstrument>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
182 <maxCharge>7</maxCharge>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
183 <minPeakLen>2</minPeakLen>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
184 <diaMinPeakLen>1</diaMinPeakLen>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
185 <useMs1Centroids>False</useMs1Centroids>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
186 <useMs2Centroids>False</useMs2Centroids>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
187 <cutPeaks>True</cutPeaks>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
188 <gapScans>1</gapScans>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
189 <minTime>NaN</minTime>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
190 <maxTime>NaN</maxTime>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
191 <matchType>MatchFromAndTo</matchType>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
192 <intensityDetermination>0</intensityDetermination>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
193 <centroidMatchTol>8</centroidMatchTol>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
194 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
195 <centroidHalfWidth>35</centroidHalfWidth>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
196 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
197 <valleyFactor>1.4</valleyFactor>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
198 <isotopeValleyFactor>1.2</isotopeValleyFactor>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
199 <advancedPeakSplitting>False</advancedPeakSplitting>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
200 <intensityThresholdMs1>0</intensityThresholdMs1>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
201 <intensityThresholdMs2>0</intensityThresholdMs2>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
202 <labelMods>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
203 <string>Arg6;Lys4</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
204 <string>Arg10;DimethLys8</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
205 </labelMods>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
206 <lcmsRunType>Standard</lcmsRunType>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
207 <reQuantify>False</reQuantify>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
208 <lfqMode>0</lfqMode>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
209 <lfqNormClusterSize>80</lfqNormClusterSize>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
210 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
211 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
212 <lfqMaxFeatures>100000</lfqMaxFeatures>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
213 <neucodeMaxPpm>0</neucodeMaxPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
214 <neucodeResolution>0</neucodeResolution>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
215 <neucodeResolutionInMda>False</neucodeResolutionInMda>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
216 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
217 <fastLfq>True</fastLfq>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
218 <lfqRestrictFeatures>False</lfqRestrictFeatures>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
219 <lfqMinRatioCount>2</lfqMinRatioCount>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
220 <maxLabeledAa>2</maxLabeledAa>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
221 <maxNmods>5</maxNmods>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
222 <maxMissedCleavages>2</maxMissedCleavages>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
223 <multiplicity>2</multiplicity>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
224 <enzymeMode>0</enzymeMode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
225 <complementaryReporterType>0</complementaryReporterType>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
226 <reporterNormalization>0</reporterNormalization>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
227 <neucodeIntensityMode>0</neucodeIntensityMode>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
228 <fixedModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
229 <string>Carbamidomethyl (C)</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
230 </fixedModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
231 <enzymes>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
232 <string>Trypsin/P</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
233 </enzymes>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
234 <enzymesFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
235 </enzymesFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
236 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
237 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
238 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
239 <variableModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
240 <string>Oxidation (M)</string>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
241 </variableModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
242 <useMultiModification>False</useMultiModification>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
243 <multiModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
244 </multiModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
245 <isobaricLabels>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
246 </isobaricLabels>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
247 <neucodeLabels>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
248 </neucodeLabels>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
249 <variableModificationsFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
250 </variableModificationsFirstSearch>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
251 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
252 <additionalVariableModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
253 </additionalVariableModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
254 <additionalVariableModificationProteins>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
255 </additionalVariableModificationProteins>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
256 <doMassFiltering>True</doMassFiltering>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
257 <firstSearchTol>20</firstSearchTol>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
258 <mainSearchTol>4.5</mainSearchTol>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
259 <searchTolInPpm>True</searchTolInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
260 <isotopeMatchTol>2</isotopeMatchTol>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
261 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
262 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
263 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
264 <checkMassDeficit>True</checkMassDeficit>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
265 <recalibrationInPpm>True</recalibrationInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
266 <intensityDependentCalibration>False</intensityDependentCalibration>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
267 <minScoreForCalibration>70</minScoreForCalibration>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
268 <matchLibraryFile>False</matchLibraryFile>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
269 <libraryFile/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
270 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
271 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
272 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
273 <reporterMassTolerance>NaN</reporterMassTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
274 <reporterPif>NaN</reporterPif>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
275 <filterPif>False</filterPif>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
276 <reporterFraction>NaN</reporterFraction>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
277 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
278 <timsHalfWidth>0</timsHalfWidth>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
279 <timsStep>0</timsStep>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
280 <timsResolution>0</timsResolution>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
281 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
282 <timsRemovePrecursor>True</timsRemovePrecursor>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
283 <timsIsobaricLabels>False</timsIsobaricLabels>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
284 <timsCollapseMsms>True</timsCollapseMsms>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
285 <crossLinkingType>0</crossLinkingType>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
286 <crossLinker/>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
287 <minMatchXl>3</minMatchXl>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
288 <minPairedPepLenXl>6</minPairedPepLenXl>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
289 <minScore_Dipeptide>40</minScore_Dipeptide>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
290 <minScore_Monopeptide>0</minScore_Monopeptide>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
291 <minScore_PartialCross>10</minScore_PartialCross>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
292 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
293 <crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
294 <isHybridPrecDetermination>False</isHybridPrecDetermination>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
295 <topXcross>3</topXcross>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
296 <doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
297 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
298 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
299 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
300 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
301 <crosslinkModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
302 </crosslinkModifications>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
303 <crosslinkFastaFiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
304 </crosslinkFastaFiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
305 <crosslinkSites>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
306 </crosslinkSites>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
307 <crosslinkNetworkFiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
308 </crosslinkNetworkFiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
309 <crosslinkMode/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
310 <peakRefinement>False</peakRefinement>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
311 <isobaricSumOverWindow>True</isobaricSumOverWindow>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
312 <isobaricWeightExponent>0.75</isobaricWeightExponent>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
313 <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
314 <diaLibraryType>0</diaLibraryType>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
315 <diaLibraryPaths>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
316 </diaLibraryPaths>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
317 <diaPeptidePaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
318 </diaPeptidePaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
319 <diaEvidencePaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
320 </diaEvidencePaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
321 <diaMsmsPaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
322 </diaMsmsPaths>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
323 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
324 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
325 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
326 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
327 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
328 <diaScoreN>7</diaScoreN>
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
329 <diaMinScore>1.99</diaMinScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
330 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
331 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
332 <centroidPosition>0</centroidPosition>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
333 <diaQuantMethod>7</diaQuantMethod>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
334 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
335 <lfqNormType>1</lfqNormType>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
336 <diaTopNForQuant>10</diaTopNForQuant>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
337 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
338 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
339 <diaPrecursorFilterType>0</diaPrecursorFilterType>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
340 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
341 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
342 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
343 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
344 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
345 <diaXgBoostEstimators>580</diaXgBoostEstimators>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
346 <diaXgBoostGamma>0.9</diaXgBoostGamma>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
347 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
348 <diaGlobalMl>True</diaGlobalMl>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
349 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
350 <diaMassWindowFactor>3.3</diaMassWindowFactor>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
351 <diaRtPrediction>False</diaRtPrediction>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
352 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
353 <diaNoMl>False</diaNoMl>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
354 <diaPermuteRt>False</diaPermuteRt>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
355 <diaPermuteCcs>False</diaPermuteCcs>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
356 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
357 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
358 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 7
diff changeset
359 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
360 <diaTransferQvalue>0.3</diaTransferQvalue>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
361 <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
362 <diaMinPeaksForRecal>5</diaMinPeaksForRecal>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
363 <diaUseFragIntensForMl>False</diaUseFragIntensForMl>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
364 <diaUseFragMassesForMl>False</diaUseFragMassesForMl>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
365 <diaMaxTrainInstances>1000000</diaMaxTrainInstances>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
366 </parameterGroup>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
367 </parameterGroups>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
368 <msmsParamsArray>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
369 <msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
370 <Name>FTMS</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
371 <MatchTolerance>20</MatchTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
372 <MatchToleranceInPpm>True</MatchToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
373 <DeisotopeTolerance>7</DeisotopeTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
374 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
375 <DeNovoTolerance>25</DeNovoTolerance>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
376 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
377 <Deisotope>True</Deisotope>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
378 <Topx>12</Topx>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
379 <TopxInterval>100</TopxInterval>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
380 <HigherCharges>True</HigherCharges>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
381 <IncludeWater>True</IncludeWater>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
382 <IncludeAmmonia>True</IncludeAmmonia>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
383 <DependentLosses>True</DependentLosses>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
384 <Recalibration>False</Recalibration>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
385 </msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
386 <msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
387 <Name>ITMS</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
388 <MatchTolerance>0.5</MatchTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
389 <MatchToleranceInPpm>False</MatchToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
390 <DeisotopeTolerance>0.15</DeisotopeTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
391 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
392 <DeNovoTolerance>0.5</DeNovoTolerance>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
393 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
394 <Deisotope>False</Deisotope>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
395 <Topx>8</Topx>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
396 <TopxInterval>100</TopxInterval>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
397 <HigherCharges>True</HigherCharges>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
398 <IncludeWater>True</IncludeWater>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
399 <IncludeAmmonia>True</IncludeAmmonia>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
400 <DependentLosses>True</DependentLosses>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
401 <Recalibration>False</Recalibration>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
402 </msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
403 <msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
404 <Name>TOF</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
405 <MatchTolerance>40</MatchTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
406 <MatchToleranceInPpm>True</MatchToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
407 <DeisotopeTolerance>0.01</DeisotopeTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
408 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
409 <DeNovoTolerance>25</DeNovoTolerance>
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
410 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
411 <Deisotope>True</Deisotope>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
412 <Topx>10</Topx>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
413 <TopxInterval>100</TopxInterval>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
414 <HigherCharges>True</HigherCharges>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
415 <IncludeWater>True</IncludeWater>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
416 <IncludeAmmonia>True</IncludeAmmonia>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
417 <DependentLosses>True</DependentLosses>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
418 <Recalibration>False</Recalibration>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
419 </msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
420 <msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
421 <Name>Unknown</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
422 <MatchTolerance>20</MatchTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
423 <MatchToleranceInPpm>True</MatchToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
424 <DeisotopeTolerance>7</DeisotopeTolerance>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
425 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 12
diff changeset
426 <DeNovoTolerance>25</DeNovoTolerance>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
427 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
428 <Deisotope>True</Deisotope>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
429 <Topx>12</Topx>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
430 <TopxInterval>100</TopxInterval>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
431 <HigherCharges>True</HigherCharges>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
432 <IncludeWater>True</IncludeWater>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
433 <IncludeAmmonia>True</IncludeAmmonia>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
434 <DependentLosses>True</DependentLosses>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
435 <Recalibration>False</Recalibration>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
436 </msmsParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
437 </msmsParamsArray>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
438 <fragmentationParamsArray>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
439 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
440 <Name>CID</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
441 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
442 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
443 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
444 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
445 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
446 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
447 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
448 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
449 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
450 <Name>HCD</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
451 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
452 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
453 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
454 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
455 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
456 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
457 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
458 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
459 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
460 <Name>ETD</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
461 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
462 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
463 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
464 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
465 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
466 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
467 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
468 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
469 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
470 <Name>PQD</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
471 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
472 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
473 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
474 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
475 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
476 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
477 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
478 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
479 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
480 <Name>ETHCD</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
481 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
482 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
483 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
484 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
485 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
486 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
487 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
488 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
489 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
490 <Name>ETCID</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
491 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
492 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
493 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
494 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
495 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
496 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
497 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
498 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
499 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
500 <Name>UVPD</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
501 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
502 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
503 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
504 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
505 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
506 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
507 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
508 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
509 <fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
510 <Name>Unknown</Name>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
511 <Connected>False</Connected>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
512 <ConnectedScore0>1</ConnectedScore0>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
513 <ConnectedScore1>1</ConnectedScore1>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
514 <ConnectedScore2>1</ConnectedScore2>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
515 <InternalFragments>False</InternalFragments>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
516 <InternalFragmentWeight>1</InternalFragmentWeight>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
517 <InternalFragmentAas>KRH</InternalFragmentAas>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
518 </fragmentationParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
519 </fragmentationParamsArray>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
520 </MaxQuantParams>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
521