Mercurial > repos > galaxyp > maxquant

diff test-data/02/mqpar.xml @ 6:2133b0be850a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
author galaxyp
date Wed, 06 May 2020 13:35:51 -0400
parents dcd39bcc7481
children d253b379322b
line wrap: on
line diff
--- a/test-data/02/mqpar.xml	Wed Apr 15 11:17:42 2020 -0400
+++ b/test-data/02/mqpar.xml	Wed May 06 13:35:51 2020 -0400
@@ -27,7 +27,7 @@
 	<lfqRequireMsms>True</lfqRequireMsms>
 	<decoyMode>revert</decoyMode>
 	<boxCarMode>all</boxCarMode>
-	<includeContaminants>True</includeContaminants>
+	<includeContaminants>False</includeContaminants>
 	<maxPeptideMass>4600</maxPeptideMass>
 	<epsilonMutationScore>True</epsilonMutationScore>
 	<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
@@ -77,15 +77,15 @@
 	<minPeptides>1</minPeptides>
 	<minRazorPeptides>1</minRazorPeptides>
 	<minUniquePeptides>0</minUniquePeptides>
-	<useCounterparts>False</useCounterparts>
+	<useCounterparts>True</useCounterparts>
 	<advancedSiteIntensities>True</advancedSiteIntensities>
 	<customProteinQuantification>False</customProteinQuantification>
 	<customProteinQuantificationFile/>
 	<minRatioCount>2</minRatioCount>
 	<restrictProteinQuantification>True</restrictProteinQuantification>
 	<restrictMods>
-		<string>Oxidation (M)</string>
-		<string>Acetyl (Protein N-term)</string>
+		<string>Pro5</string>
+		<string>Pro6</string>
 	</restrictMods>
 	<matchingTimeWindow>0</matchingTimeWindow>
 	<matchingIonMobilityWindow>0</matchingIonMobilityWindow>
@@ -93,7 +93,7 @@
 	<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
 	<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
 	<compositionPrediction>0</compositionPrediction>
-	<quantMode>1</quantMode>
+	<quantMode>0</quantMode>
 	<massDifferenceMods>
    </massDifferenceMods>
 	<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
@@ -267,7 +267,7 @@
 			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
 			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
 			<reporterMassTolerance>0.003</reporterMassTolerance>
-			<reporterPif>0</reporterPif>
+			<reporterPif>0.6</reporterPif>
 			<filterPif>False</filterPif>
 			<reporterFraction>0</reporterFraction>
 			<reporterBasePeakRatio>0</reporterBasePeakRatio>
@@ -442,8 +442,8 @@
 			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
 			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
 			<reporterMassTolerance>0.003</reporterMassTolerance>
-			<reporterPif>0</reporterPif>
-			<filterPif>False</filterPif>
+			<reporterPif>0.8</reporterPif>
+			<filterPif>True</filterPif>
 			<reporterFraction>0</reporterFraction>
 			<reporterBasePeakRatio>0</reporterBasePeakRatio>
 			<timsHalfWidth>0</timsHalfWidth>