Mercurial > repos > galaxyp > maxquant

diff test-data/02/mqpar.xml @ 7:d253b379322b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
author galaxyp
date Mon, 01 Jun 2020 11:51:25 -0400
parents 2133b0be850a
children 0839f84def5e
line wrap: on
line diff
--- a/test-data/02/mqpar.xml	Wed May 06 13:35:51 2020 -0400
+++ b/test-data/02/mqpar.xml	Mon Jun 01 11:51:25 2020 -0400
@@ -25,7 +25,7 @@
 	<separateLfq>False</separateLfq>
 	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
 	<lfqRequireMsms>True</lfqRequireMsms>
-	<decoyMode>revert</decoyMode>
+	<decoyMode>randomize</decoyMode>
 	<boxCarMode>all</boxCarMode>
 	<includeContaminants>False</includeContaminants>
 	<maxPeptideMass>4600</maxPeptideMass>
@@ -68,11 +68,11 @@
    </intensityPredictionsFile>
 	<minPepLen>7</minPepLen>
 	<psmFdrCrosslink>0.01</psmFdrCrosslink>
-	<peptideFdr>0.01</peptideFdr>
-	<proteinFdr>0.01</proteinFdr>
+	<peptideFdr>0.5</peptideFdr>
+	<proteinFdr>0.4</proteinFdr>
 	<siteFdr>0.01</siteFdr>
-	<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
-	<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
+	<minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>
+	<maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch>
 	<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
 	<minPeptides>1</minPeptides>
 	<minRazorPeptides>1</minRazorPeptides>
@@ -267,7 +267,7 @@
 			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
 			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
 			<reporterMassTolerance>0.003</reporterMassTolerance>
-			<reporterPif>0.6</reporterPif>
+			<reporterPif>0</reporterPif>
 			<filterPif>False</filterPif>
 			<reporterFraction>0</reporterFraction>
 			<reporterBasePeakRatio>0</reporterBasePeakRatio>