Mercurial > repos > iuc > bedtools

comparison linksBed.xml @ 0:4fb5ea02b441 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
parents
children 7511823bdea1
comparison
equal deleted inserted replaced
-1:000000000000 0:4fb5ea02b441
1 <tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 linksBed
10 -base $basename
11 -org $org
12 -db $db
13 -i $inputA
14 &gt; $output
15 </command>
16 <inputs>
17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
18 <param name="basename" type="text" value="http://genome.ucsc.edu" label="The “basename” for the UCSC browser" />
19 <param name="org" type="text" value="human" label="The organism (e.g. mouse, human)" />
20 <param name="db" type="text" value="hg18" label="The genome build" />
21 </inputs>
22 <outputs>
23 <data name="output" format="html" />
24 </outputs>
25 <help>
26
27 **What it does**
28
29 Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.
30
31 @REFERENCES@
32 </help>
33 </tool>