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comparison linksBed.xml @ 0:b8348686a0b9 draft

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Imported from capsule None
author iuc
date Tue, 04 Nov 2014 01:45:04 -0500
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children 82aac94b06c3
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-1:000000000000 0:b8348686a0b9
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 <expand macro="citations" />
34 </tool>