<tool id="allele_counts_1" version="1.0" name="Count alleles">
  <description>and minor allele frequencies</description>
  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header</command>
  <inputs>
    <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
    <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold"/>
    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (per strand)"/>
    <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="False" label="Write header line" />
  </inputs>
  <outputs>
    <data name="output" format="tabular"/>
  </outputs>
  <stdio>
    <exit_code range="1:" err_level="fatal"/>
    <exit_code range=":-1" err_level="fatal"/>
  </stdio>

  <help>
This tool parses the output of Naive Variant Detector, counting variants, calculating numbers of alleles, and minor allele frequency. It applies filters based on coverage, strand bias, and minor allele frequency cutoffs.

**Note**: The VCF file from the Naive Variant Detector must include counts *per strand*.
  </help>

</tool>