# HG changeset patch
# User jjohnson
# Date 1658605453 0
# Node ID c2689aeefa3aec062a2578bf40ee3a4d41697a54
# Parent  82fde491fe9100aec34deb491b2d9734e96546f4
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 315f6ba609e9545c3a374f7fd471aee50b135ec8-dirty"

diff -r 82fde491fe91 -r c2689aeefa3a macros.xml
--- a/macros.xml	Wed Jun 15 17:31:00 2022 +0000
+++ b/macros.xml	Sat Jul 23 19:44:13 2022 +0000
@@ -20,23 +20,23 @@
         <version_command>rmats.py --version</version_command>
     </xml>
     
-    <token name="COLNAMES_SUMMARY">EventType,TotalEventsJC,TotalEventsJCEC,SignificantEventsJC,SigEventsJCSample1HigherInclusion,SigEventsJCSample2HigherInclusion,SignificantEventsJCEC,SigEventsJCECSample1HigherInclusion,SigEventsJCECSample2HigherInclusion</token>
-    <token name="SHAREDCOLS">ID,GeneID,geneSymbol,chr,strand</token>
-    <token name="MXECOLS">1stExonStart_0base,1stExonEnd,2ndExonStart_0base,2ndExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
-    <token name="SECOLS">exonStart_0base,exonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
-    <token name="ACOLS">longExonStart_0base,longExonEnd,shortES,shortEE,flankingES,flankingEE</token>
-    <token name="RICOLS">riExonStart_0base,riExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
-    <token name="CNTCOLS">ID,IJC_SAMPLE_1,SJC_SAMPLE_1,IJC_SAMPLE_2,SJC_SAMPLE_2,IncFormLen,SkipFormLen</token>
-    <token name="STATCOLS">PValue,FDR,IncLevel1,IncLevel2,IncLevelDifference</token>
-    <token name="SAMPLECOLS">@CNTCOLS@,@STATCOLS@</token>
-    <token name="COLNAMES_MXE_GTF">@SHAREDCOLS@,@MXECOLS@</token>
-    <token name="COLNAMES_MXE">@SHAREDCOLS@,@MXECOLS@,@SAMPLECOLS@</token>
-    <token name="COLNAMES_SE_GTF">@SHAREDCOLS@,@SECOLS@</token>
-    <token name="COLNAMES_SE">@SHAREDCOLS@,@SECOLS@,@SAMPLECOLS@</token>
-    <token name="COLNAMES_A_SS_GTF">@SHAREDCOLS@,@ACOLS@</token>
-    <token name="COLNAMES_A_SS">@SHAREDCOLS@,@ACOLS@,@SAMPLECOLS@</token>
-    <token name="COLNAMES_RI_GTF">@SHAREDCOLS@,@RICOLS@</token>
-    <token name="COLNAMES_RI">@SHAREDCOLS@,@RICOLS@,@SAMPLECOLS@</token>
+    <token name="@COLNAMES_SUMMARY@">EventType,TotalEventsJC,TotalEventsJCEC,SignificantEventsJC,SigEventsJCSample1HigherInclusion,SigEventsJCSample2HigherInclusion,SignificantEventsJCEC,SigEventsJCECSample1HigherInclusion,SigEventsJCECSample2HigherInclusion</token>
+    <token name="@SHAREDCOLS@">ID,GeneID,geneSymbol,chr,strand</token>
+    <token name="@MXECOLS@">1stExonStart_0base,1stExonEnd,2ndExonStart_0base,2ndExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
+    <token name="@SECOLS@">exonStart_0base,exonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
+    <token name="@ACOLS@">longExonStart_0base,longExonEnd,shortES,shortEE,flankingES,flankingEE</token>
+    <token name="@RICOLS@">riExonStart_0base,riExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
+    <token name="@CNTCOLS@">ID,IJC_SAMPLE_1,SJC_SAMPLE_1,IJC_SAMPLE_2,SJC_SAMPLE_2,IncFormLen,SkipFormLen</token>
+    <token name="@STATCOLS@">PValue,FDR,IncLevel1,IncLevel2,IncLevelDifference</token>
+    <token name="@SAMPLECOLS@">@CNTCOLS@,@STATCOLS@</token>
+    <token name="@COLNAMES_MXE_GTF@">@SHAREDCOLS@,@MXECOLS@</token>
+    <token name="@COLNAMES_MXE@">@SHAREDCOLS@,@MXECOLS@,@SAMPLECOLS@</token>
+    <token name="@COLNAMES_SE_GTF@">@SHAREDCOLS@,@SECOLS@</token>
+    <token name="@COLNAMES_SE@">@SHAREDCOLS@,@SECOLS@,@SAMPLECOLS@</token>
+    <token name="@COLNAMES_A_SS_GTF@">@SHAREDCOLS@,@ACOLS@</token>
+    <token name="@COLNAMES_A_SS@">@SHAREDCOLS@,@ACOLS@,@SAMPLECOLS@</token>
+    <token name="@COLNAMES_RI_GTF@">@SHAREDCOLS@,@RICOLS@</token>
+    <token name="@COLNAMES_RI@">@SHAREDCOLS@,@RICOLS@,@SAMPLECOLS@</token>
 
     <xml name="output_actions" token_column_names="@COLNAME_SUMMARY@">
         <actions>