comparison GVF2VCF.xml @ 0:18d965813efc default tip

intial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:37:21 -0600
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1 <?xml version="1.0"?>
2
3 <tool id="gvf_to_vcf_1" name="Convert diBayes GVF file to VCF format">
4 <version_string>dibayes_gff2vcf -v</version_string>
5 <command interpreter="perl">dibayes_gff2vcf $input_gff $output_vcf</command>
6 <inputs>
7 <param format="gff3" name="input_gff" type="data" label="GVF file generated by diBayes (may work for other, but untested)"/>
8 </inputs>
9 <outputs>
10 <data format="vcf" name="output_vcf" label="diBayes calls in VCF format"/>
11 </outputs>
12
13 <tests>
14 <test>
15 <param name="input_gff" value="depth_test.bam" ftype="gff"/>
16 <output name="output_vcf">
17 <assert_contents>
18 <has_text text="targeted nucleotide bases: 155091"/>
19 <has_text text="bases mapped to targeted regions: 11473773"/>
20 <has_text text="bases with less than 20-fold coverage: 19046"/>
21 </assert_contents>
22 </output>
23 </test>
24 </tests>
25
26 <help>
27 This tool an ABI colorspace sequencing run's variant calls (using LifeScope's diBayes) into a format amenable to many variant processing tools.
28 </help>
29
30 </tool>