comparison mytools/collapseBed.xml @ 0:39217fa39ff2

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author xuebing
date Tue, 13 Mar 2012 23:34:52 -0400
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1 <tool id="collapseBed" name="collapse">
2 <description>intervals</description>
3 <command interpreter="python">collapseBed2.py $input $strand $score > $outfile </command>
4 <inputs>
5 <param name="input" format="interval" type="data" label="Original file"/>
6 <param name="strand" size="10" type="integer" value="6" label="strand column" help="set 0 to ignore strand information" />
7 <param name="score" size="10" type="integer" value="5" label="for duplicate lines, keep the one with max value in column" help="set 0 to ignore score information" />
8 </inputs>
9 <outputs>
10 <data format="input" name="outfile" />
11 </outputs>
12 <help>
13
14 **What it does**
15
16 This tool collapses genomic intervals that have the same position (and strandness if specified) and output a set of unique intervals.
17
18 </help>
19 </tool>