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planemo upload for repository https://github.com/remimarenco/bedclip
author rmarenco
date Sat, 23 Jul 2016 03:20:57 -0400
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-1:000000000000 0:3275f20f1368
1 <tool id="bedclip" name="bedClip" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
4 <requirement type="package" version="324">ucsc-twobitinfo</requirement>
5 <requirement type="package" version="332">ucsc-bedclip</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command><![CDATA[
11 faToTwoBit "$ref_genome" two_bit_ref_genome;
12 twoBitInfo two_bit_ref_genome chrom_sizes;
13 bedClip "$bed_file" chrom_sizes "$bed_clipped";
14 ]]></command>
15 <inputs>
16 <param type="data" name="ref_genome" format="fasta" />
17 <param type="data" name="bed_file" format="bed" />
18 </inputs>
19 <outputs>
20 <data name="bed_clipped" format="bed" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="ref_genome" value="input.fasta"/>
25 <param name="bed_file" value="input.bed"/>
26 <output name="bed_clipped" file="output.bed"/>
27 </test>
28 </tests>
29 <help><![CDATA[
30 ]]></help>
31 </tool>