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annotate macros.xml @ 0:82fde491fe91 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
author jjohnson
date Wed, 15 Jun 2022 17:31:00 +0000
parents
children c2689aeefa3a
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82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
jjohnson
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1 <macros>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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2 <token name="@TOOL_VERSION@">4.1.2</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="requirements">
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5 <requirements>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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6 <requirement type="package" version="@TOOL_VERSION@">rmats</requirement>
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7 <requirement type="package" version="4.0">r-base</requirement>
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8 <yield/>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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9 </requirements>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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10 </xml>
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11 <xml name="citations">
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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12 <citations>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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13 <citation type="doi">10.1073/pnas.1419161111</citation>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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14 <citation type="doi">10.1007/978-1-62703-514-9_10</citation>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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15 <citation type="doi">10.1093/nar/gkr1291</citation>
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16 <yield />
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17 </citations>
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18 </xml>
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19 <xml name="version_command">
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20 <version_command>rmats.py --version</version_command>
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21 </xml>
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22
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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23 <token name="COLNAMES_SUMMARY">EventType,TotalEventsJC,TotalEventsJCEC,SignificantEventsJC,SigEventsJCSample1HigherInclusion,SigEventsJCSample2HigherInclusion,SignificantEventsJCEC,SigEventsJCECSample1HigherInclusion,SigEventsJCECSample2HigherInclusion</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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24 <token name="SHAREDCOLS">ID,GeneID,geneSymbol,chr,strand</token>
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25 <token name="MXECOLS">1stExonStart_0base,1stExonEnd,2ndExonStart_0base,2ndExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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26 <token name="SECOLS">exonStart_0base,exonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
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27 <token name="ACOLS">longExonStart_0base,longExonEnd,shortES,shortEE,flankingES,flankingEE</token>
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28 <token name="RICOLS">riExonStart_0base,riExonEnd,upstreamES,upstreamEE,downstreamES,downstreamEE</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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29 <token name="CNTCOLS">ID,IJC_SAMPLE_1,SJC_SAMPLE_1,IJC_SAMPLE_2,SJC_SAMPLE_2,IncFormLen,SkipFormLen</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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30 <token name="STATCOLS">PValue,FDR,IncLevel1,IncLevel2,IncLevelDifference</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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31 <token name="SAMPLECOLS">@CNTCOLS@,@STATCOLS@</token>
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32 <token name="COLNAMES_MXE_GTF">@SHAREDCOLS@,@MXECOLS@</token>
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33 <token name="COLNAMES_MXE">@SHAREDCOLS@,@MXECOLS@,@SAMPLECOLS@</token>
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34 <token name="COLNAMES_SE_GTF">@SHAREDCOLS@,@SECOLS@</token>
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35 <token name="COLNAMES_SE">@SHAREDCOLS@,@SECOLS@,@SAMPLECOLS@</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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36 <token name="COLNAMES_A_SS_GTF">@SHAREDCOLS@,@ACOLS@</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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37 <token name="COLNAMES_A_SS">@SHAREDCOLS@,@ACOLS@,@SAMPLECOLS@</token>
82fde491fe91 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 8450d297d5845dda910bd748bde3b12156b6d6ec-dirty"
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38 <token name="COLNAMES_RI_GTF">@SHAREDCOLS@,@RICOLS@</token>
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39 <token name="COLNAMES_RI">@SHAREDCOLS@,@RICOLS@,@SAMPLECOLS@</token>
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40
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41 <xml name="output_actions" token_column_names="@COLNAME_SUMMARY@">
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42 <actions>
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43 <action name="comment_lines" type="metadata" default="1" />
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44 <action name="column_names" type="metadata" default="@COLUMN_NAMES@" />
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45 </actions>
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46 </xml>
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47
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48 </macros>