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comparison defuse_results_to_vcf.xml @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
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10:f65857c1b92e 11:b22f8634ff84
1 <?xml version="1.0"?>
2 <tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="0.6.1">
3 <description>generate a VCF from a DeFuse Results file</description>
4 <requirements>
5 <requirement type="package" version="0.6.1">defuse</requirement>
6 </requirements>
7 <command interpreter="python">defuse_results_to_vcf.py --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
8 </command>
9 <inputs>
10 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/>
11 </inputs>
12 <stdio>
13 <exit_code range="1:" level="fatal" description="Error" />
14 </stdio>
15 <outputs>
16 <data name="vcf" metadata_source="defuse_results" format="vcf"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
21 <output name="vcf" file="mm10_results.filtered.vcf"/>
22 </test>
23 </tests>
24 <help>
25 **Defuse Results to VCF**
26
27 Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file.
28
29 This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file.
30
31 .. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
32 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
33 </help>
34 </tool>