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comparison 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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-1:000000000000 0:ff15d6def09b
1 <macros>
2 <token name="@TOOL_VERSION@">4.1.2</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">rmats</requirement>
7 <requirement type="package" version="4.0">r-base</requirement>
8 <yield/>
9 </requirements>
10 </xml>
11 <xml name="citations">
12 <citations>
13 <citation type="doi">10.1073/pnas.1419161111</citation>
14 <citation type="doi">10.1007/978-1-62703-514-9_10</citation>
15 <citation type="doi">10.1093/nar/gkr1291</citation>
16 <yield />
17 </citations>
18 </xml>
19 <xml name="version_command">
20 <version_command>rmats.py --version</version_command>
21 </xml>
22
23 <token name="@COLNAMES_SUMMARY@">EventType,TotalEventsJC,TotalEventsJCEC,SignificantEventsJC,SigEventsJCSample1HigherInclusion,SigEventsJCSample2HigherInclusion,SignificantEventsJCEC,SigEventsJCECSample1HigherInclusion,SigEventsJCECSample2HigherInclusion</token>
24 <token name="@SHAREDCOLS@">ID,GeneID,geneSymbol,chr,strand</token>
25 <token name="@MXECOLS@">1stExonStart_0base,1stExonEnd,2ndExonStart_0base,2ndExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
26 <token name="@SECOLS@">exonStart_0base,exonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
27 <token name="@ACOLS@">longExonStart_0base,longExonEnd,shortES,shortEE,flankingES,flankingEE</token>
28 <token name="@RICOLS@">riExonStart_0base,riExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
29 <token name="@CNTCOLS@">ID,IJC_SAMPLE_1,SJC_SAMPLE_1,IJC_SAMPLE_2,SJC_SAMPLE_2,IncFormLen,SkipFormLen</token>
30 <token name="@STATCOLS@">PValue,FDR,IncLevel1,IncLevel2,IncLevelDifference</token>
31 <token name="@SAMPLECOLS@">@CNTCOLS@,@STATCOLS@</token>
32 <token name="@COLNAMES_MXE_GTF@">@SHAREDCOLS@,@MXECOLS@</token>
33 <token name="@COLNAMES_MXE@">@SHAREDCOLS@,@MXECOLS@,@SAMPLECOLS@</token>
34 <token name="@COLNAMES_SE_GTF@">@SHAREDCOLS@,@SECOLS@</token>
35 <token name="@COLNAMES_SE@">@SHAREDCOLS@,@SECOLS@,@SAMPLECOLS@</token>
36 <token name="@COLNAMES_A_SS_GTF@">@SHAREDCOLS@,@ACOLS@</token>
37 <token name="@COLNAMES_A_SS@">@SHAREDCOLS@,@ACOLS@,@SAMPLECOLS@</token>
38 <token name="@COLNAMES_RI_GTF@">@SHAREDCOLS@,@RICOLS@</token>
39 <token name="@COLNAMES_RI@">@SHAREDCOLS@,@RICOLS@,@SAMPLECOLS@</token>
40
41 <xml name="output_actions" token_column_names="@COLNAME_SUMMARY@">
42 <actions>
43 <action name="comment_lines" type="metadata" default="1" />
44 <action name="column_names" type="metadata" default="@COLUMN_NAMES@" />
45 </actions>
46 </xml>
47
48 </macros>