<?xml version="1.0"?>

<tool id="hgvs2vcf_1" name="Convert a variant table with HGVS syntax into a VCF">
  <version_string>echo 1.0.0</version_string>
  <command interpreter="perl">hgvs_to_vcf $in_hgvs_table $output_vcf $sample_name hg19
  </command>
  <inputs>
    <param name="in_hgvs_table" format="achri_snp_table" type="data" label="SNP table with HGVS calls"/>
    <param type="text" name="sample_name" value="ANON" label="Name for the sample in the output VCF file's header"/>
  </inputs>
  <outputs>
    <data format="vcf" name="output_vcf" type="data" label="Sequence variant calls"/>
  </outputs>

  <tests>
  </tests>

  <help>This tools converts the tabular format used to describe variants and associate annotation at ACHRI into a standard Variant Calls Format (VCF) version 4.1 file, which is accepted by many genetic analysis programs.</help>
</tool>