<tool id="varscan" name="VarScan Readcount" version="2.4.4">
    <description>To use varscan readcount tool</description>

    <requirements>
        <requirement type="package" version="2.4.4">varscan</requirement>
    </requirements>

    <stdio>
        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <version_command><![CDATA[
varscan 2>&1 | head -n 1
    ]]></version_command>

    <command><![CDATA[
        varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
    ]]></command>

    <inputs>
        <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
        <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 [1]"/>
        <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
    </inputs>

    <outputs>
        <data name="output" format="vcf"/>
    </outputs>

    <help>

command: varscan readcounts --help

Min coverage:   1
Min base qual:  20
USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS
        OPTIONS:
        --variants-file A list of variants at which to report readcounts
        --output-file   Output file to contain the readcounts
        --min-coverage  Minimum read depth at a position to make a call [1]
        --min-base-qual Minimum base quality at a position to count a read [20]

    </help>

    <citations>
        <citation type="doi">10.1101/gr.129684.111</citation>
    </citations>
</tool>