Mercurial > repos > xiaoyi-cao > annotatebed

comparison annotateBedWrapper.xml @ 8:57a9a34af5ce draft

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author xiaoyi-cao
date Sun, 02 Dec 2012 15:11:35 -0500
parents 7a516a36a25a
children 6935cb1ed000
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7:7a516a36a25a 8:57a9a34af5ce
2 2
3 <description>Annotate BED files with overlapping BED files</description> 3 <description>Annotate BED files with overlapping BED files</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="binary">annotateBed</requirement> 6 <requirement type="binary">annotateBed</requirement>
7 <requirement type="package">bedtools</requirement>
7 </requirements> 8 </requirements>
8 9
9 <command> 10 <command>
10 annotateBed 11 annotateBed
11 $countflag 12 $countflag
12 -i '$inputRegion' 13 -i '$inputRegion'
13 -names 14 -names
14 #for $i, $s in enumerate($annotateColumn) 15 #for $i, $s in enumerate($annotateColumn)
15 ${s.colname} 16 '${s.colname}'
16 #end for 17 #end for
17 -files 18 -files
18 #for $i, $s in enumerate($annotateColumn) 19 #for $i, $s in enumerate($annotateColumn)
19 ${s.colfile} 20 '${s.colfile}'
20 #end for 21 #end for
21 &gt; '$output' 22 &gt; '$output'
22 </command> 23 </command>
23 24
24 <inputs> 25 <inputs>