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diff macros.xml @ 0:ff15d6def09b draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 315f6ba609e9545c3a374f7fd471aee50b135ec8-dirty"
author jjohnson
date Sat, 23 Jul 2022 21:23:48 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Jul 23 21:23:48 2022 +0000
@@ -0,0 +1,48 @@
+<macros>
+    <token name="@TOOL_VERSION@">4.1.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rmats</requirement>
+        <requirement type="package" version="4.0">r-base</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1073/pnas.1419161111</citation>
+            <citation type="doi">10.1007/978-1-62703-514-9_10</citation>
+            <citation type="doi">10.1093/nar/gkr1291</citation>
+            <yield />
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <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>
+
+    <xml name="output_actions" token_column_names="@COLNAME_SUMMARY@">
+        <actions>
+            <action name="comment_lines" type="metadata" default="1" />
+            <action name="column_names" type="metadata" default="@COLUMN_NAMES@" />
+        </actions>
+    </xml>
+
+</macros>