Mercurial > repos > yusuf > gvf_to_vcf
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GVF2VCF.xml Wed Mar 25 13:37:21 2015 -0600 @@ -0,0 +1,30 @@ +<?xml version="1.0"?> + +<tool id="gvf_to_vcf_1" name="Convert diBayes GVF file to VCF format"> + <version_string>dibayes_gff2vcf -v</version_string> + <command interpreter="perl">dibayes_gff2vcf $input_gff $output_vcf</command> + <inputs> + <param format="gff3" name="input_gff" type="data" label="GVF file generated by diBayes (may work for other, but untested)"/> + </inputs> + <outputs> + <data format="vcf" name="output_vcf" label="diBayes calls in VCF format"/> + </outputs> + + <tests> + <test> + <param name="input_gff" value="depth_test.bam" ftype="gff"/> + <output name="output_vcf"> + <assert_contents> + <has_text text="targeted nucleotide bases: 155091"/> + <has_text text="bases mapped to targeted regions: 11473773"/> + <has_text text="bases with less than 20-fold coverage: 19046"/> + </assert_contents> + </output> + </test> + </tests> + + <help> +This tool an ABI colorspace sequencing run's variant calls (using LifeScope's diBayes) into a format amenable to many variant processing tools. + </help> + +</tool>