# HG changeset patch
# User jjohnson
# Date 1658611428 0
# Node ID ff15d6def09b6f1955fb2bb61aa2f76f96395cb9
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 315f6ba609e9545c3a374f7fd471aee50b135ec8-dirty"
diff -r 000000000000 -r ff15d6def09b macros.xml
--- /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 @@
+
+ 4.1.2
+ 0
+
+
+ rmats
+ r-base
+
+
+
+
+
+ 10.1073/pnas.1419161111
+ 10.1007/978-1-62703-514-9_10
+ 10.1093/nar/gkr1291
+
+
+
+
+ rmats.py --version
+
+
+ EventType,TotalEventsJC,TotalEventsJCEC,SignificantEventsJC,SigEventsJCSample1HigherInclusion,SigEventsJCSample2HigherInclusion,SignificantEventsJCEC,SigEventsJCECSample1HigherInclusion,SigEventsJCECSample2HigherInclusion
+ ID,GeneID,geneSymbol,chr,strand
+ 1stExonStart_0base,1stExonEnd,2ndExonStart_0base,2ndExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE
+ exonStart_0base,exonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE
+ longExonStart_0base,longExonEnd,shortES,shortEE,flankingES,flankingEE
+ riExonStart_0base,riExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE
+ ID,IJC_SAMPLE_1,SJC_SAMPLE_1,IJC_SAMPLE_2,SJC_SAMPLE_2,IncFormLen,SkipFormLen
+ PValue,FDR,IncLevel1,IncLevel2,IncLevelDifference
+ @CNTCOLS@,@STATCOLS@
+ @SHAREDCOLS@,@MXECOLS@
+ @SHAREDCOLS@,@MXECOLS@,@SAMPLECOLS@
+ @SHAREDCOLS@,@SECOLS@
+ @SHAREDCOLS@,@SECOLS@,@SAMPLECOLS@
+ @SHAREDCOLS@,@ACOLS@
+ @SHAREDCOLS@,@ACOLS@,@SAMPLECOLS@
+ @SHAREDCOLS@,@RICOLS@
+ @SHAREDCOLS@,@RICOLS@,@SAMPLECOLS@
+
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+
diff -r 000000000000 -r ff15d6def09b rmats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rmats.xml Sat Jul 23 21:23:48 2022 +0000
@@ -0,0 +1,269 @@
+
+ detect differential alternative splicing events from RNA-Seq
+
+ macros.xml
+
+
+
+ b1.txt &&
+ #if $b2
+ echo $b2 > b2.txt &&
+ #end if
+ rmats.py
+ --b1 b1.txt
+ #if $b2
+ --b1 b1.txt
+ #end if
+ --gtf '$gtf'
+ #if $novel.novelSS == 'yes'
+ --novelSS
+ #if $novel.mil
+ --mil $novel.mil
+ #end if
+ #if $novel.mel
+ --mel $novel.mel
+ #end if
+ #end if
+ #if $readLength
+ --readLength $readLength
+ #end if
+ $variable_read_length
+ #if $libType
+ --libType "$libType"
+ #end if
+ #if $anchorLength
+ --anchorLength $anchorLength
+ #end if
+ #if $cstat
+ --cstat $cstat
+ #end if
+ $paired_stats
+ --nthread \${GALAXY_SLOTS:-1}
+ --tmp tmp
+ --od outputs
+ ]]>
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+ history_outputs and 'fromGTF.SE.txt' in history_outputs
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+ history_outputs and 'fromGTF.A3SS.txt' in history_outputs
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+ history_outputs and 'fromGTF.A5SS.txt' in history_outputs
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+ history_outputs and 'fromGTF.MXE.txt' in history_outputs
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+ history_outputs and 'fromGTF.RI.txt' in history_outputs
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+ history_outputs and 'fromGTF.novelSpliceSite.SE.txt' in history_outputs
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+ history_outputs and 'fromGTF.novelSpliceSite.A3SS.txt' in history_outputs
+
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+ history_outputs and 'fromGTF.novelSpliceSite.A5SS.txt' in history_outputs
+
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+ history_outputs and 'fromGTF.novelSpliceSite.MXE.txt' in history_outputs
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+ history_outputs and 'fromGTF.novelSpliceSite.RI.txt' in history_outputs
+
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+ history_outputs and 'fromGTF.novelJunction.SE.txt' in history_outputs
+
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+ history_outputs and 'fromGTF.novelJunction.A3SS.txt' in history_outputs
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+ history_outputs and 'fromGTF.novelJunction.A5SS.txt' in history_outputs
+
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+ history_outputs and 'fromGTF.novelJunction.MXE.txt' in history_outputs
+
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+ history_outputs and 'fromGTF.novelJunction.RI.txt' in history_outputs
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+ history_outputs and 'SE.MATS.JCEC.txt' in history_outputs
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+ history_outputs and 'SE.MATS.JC.txt' in history_outputs
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+ history_outputs and 'A3SS.MATS.JCEC.txt' in history_outputs
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+ history_outputs and 'A3SS.MATS.JC.txt' in history_outputs
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+ history_outputs and 'A5SS.MATS.JCEC.txt' in history_outputs
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+ history_outputs and 'A5SS.MATS.JC.txt' in history_outputs
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+ history_outputs and 'MXE.MATS.JCEC.txt' in history_outputs
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+ history_outputs and 'MXE.MATS.JC.txt' in history_outputs
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+ history_outputs and 'RI.MATS.JCEC.txt' in history_outputs
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+ history_outputs and 'RI.MATS.JC.txt' in history_outputs
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