comparison mytools/closestBed.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="closestbed" name="closestBed">
2 <description>find closest features</description>
3 <command>closestBed -a $inputa -b $inputb $strandness -d $no -t $tie> $output_data
4 </command>
5 <inputs>
6 <param name="inputa" type="data" format="interval,bam,bed,gff,vcf" label="Input A (-a)"/>
7 <param name="inputb" type="data" format="interval,bam,bed,gff,vcf" label="Input B (-b)"/>
8 <param name="strandness" type="select" label="Strand requirement" >
9 <option value="" selected="true"> none </option>
10 <option value="-s" > -s: closest feature on the same strand</option>
11 <option value="-S" > -S: closest feature on the opposite strand </option>
12 </param>
13
14 <param name="no" label="Only look for non-overlaping features" type="boolean" truevalue="-no" falsevalue="" checked="False"/>
15 <param name="tie" type="select" label="Strand requirement" >
16 <option value="all" selected="true"> report all ties </option>
17 <option value="first" > report the first that occurred</option>
18 <option value="last" > report the last that occurred </option>
19 </param>
20 </inputs>
21 <outputs>
22 <data format="input" name="output_data"/>
23 </outputs>
24 <help>
25
26 **What it does**
27
28 This is a wrapper for closestBed.
29
30 </help>
31 </tool>
32