Mercurial > repos > yusuf > gvf_to_vcf
comparison GVF2VCF.xml @ 0:18d965813efc default tip
intial commit
author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:37:21 -0600 |
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-1:000000000000 | 0:18d965813efc |
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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> |