comparison ExtendBedRegions.xml @ 0:cb1c17dddc14 default tip

initial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:32:42 -0600
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-1:000000000000 0:cb1c17dddc14
1 <?xml version="1.0"?>
2
3 <tool id="extend_bed_regions_1" name="Expand or contract regions">
4 <description>in a BED file by a fixed number of bases</description>
5 <version_string>echo 1.0.0</version_string>
6 <command interpreter="perl">extend_bed_regions $in_bed $extent $strand $out_bed</command>
7 <inputs>
8 <param format="bed" name="in_bed" type="data" label="BED file whose regions should be modified"/>
9 <param name="extent" type="integer" value="50" label="Number of bases to extend each BED region (negative values cause contraction)"/>
10 <param name="strand" type="select" display="radio" label="Which end to extend?" help="If the BED file contains strand info, extension will be strand specific. Otherwise, the positive strand is assumed">
11 <option value="5">5'</option>
12 <option value="3">3'</option>
13 <option value="both" selected="true">Both</option>
14 </param>
15 </inputs>
16 <outputs>
17 <data name="out_bed" format="bed" type="data" label="BED file with extended/contracted regions"/>
18 </outputs>
19
20 <tests/>
21
22 <help>
23 This tool expands each regions defined in a BED file by the specified amount, at the specified end(s). If expanded regions overlap, they are merged.
24 </help>
25
26 </tool>