<tool id="varscan" name="VarScan Readcount" version="3">
  <description>To use varscan readcount tool</description>
  <requirements>
    <requirement type="package" version="2.4.4">varscan</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    varscan readcounts '${input}' --min-coverage '${min_cov}' --min-base-qual ${min_base_qual} --output-file '${output}'
  ]]></command>
  <inputs>
    <param name="input" format="pileup" type="data" label="Pileup dataset"/>
    <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call (default: 1)"/>
    <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" help="Minimum base quality at a position to count a read (default: 20)"/>
  </inputs>
  <outputs>
    <data name="output" format="vcf"/>
  </outputs>
  <help>
    USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS

    OPTIONS:

      --output-file   Output file to contain the readcounts

      --min-coverage  Minimum read depth at a position to make a call (default: 1)

      --min-base-qual Minimum base quality at a position to count a read (default: 20)

  </help>
</tool>