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author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:09:20 -0600
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1 <?xml version="1.0"?>
2
3 <tool id="add_names_to_bed_1" name="Add names to a BED file">
4 <description>based on overlap with a named regions BED file</description>
5 <version_string>echo 1.0.0</version_string>
6 <command interpreter="perl">add_names_to_bed $in_unnamed_bed $in_named_bed $out_renamed_bed $out_log</command>
7 <inputs>
8 <param format="bed" name="in_unnamed_bed" type="data" label="BED file to rename" help="BED file without useful names for each region reported"/>
9 <param format="bed" name="in_named_bed" type="data" label="BED file with names to inherit" help="BED file with useful names for each region (4th column)"/>
10 </inputs>
11 <outputs>
12 <data name="out_renamed_bed" format="bed" type="data" label="BED file with renamed regions"/>
13 <data name="out_log" format="text" type="data" label="Renaming stats"/>
14 </outputs>
15
16 <tests/>
17
18 <help>
19 This tool replaces names (4th column) in a BED file, based on overlap of those regions with named regions
20 provided in another BED file. For example, a list of exome dud regions could be annotated with the gene
21 names in the dud regions, by running this tool with the UCSC refFlat BED file as the named regions source.
22 </help>
23
24 </tool>