<?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>