<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">varscan</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@VERSION@">2.4.3</token>

    <xml name="stdio">
        <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>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.129684.111</citation>
            <citation type="doi">10.1002/0471250953.bi1504s44</citation>
        </citations>
    </xml>

    <xml name="input_pileups">
        <conditional name="pileup">
           <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help="">
               <option value="separated">As separated normal and tumor files</option>
               <option value="combined">Normal and Tumor combined in one file</option>
           </param>
           <when value="separated">
                <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/>
                <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/>
           </when>
           <when value="combined">
                <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/>
           </when>
        </conditional>
    </xml>

    <token name="@INPUT_PILEUPS@">
        #if $pileup.pileup_select == 'separated'
           '${pileup.normal_pileup}'
           '${pileup.tumor_pileup}'
           galaxy_out
        #else:
           '${pileup.combined_pileup}'
            galaxy_out
           --mpileup 1
        #end if
        
    </token>

    <xml name="min_coverage" token_help="Minimum depth at a position to make a call">
        <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
            label="Minimum coverage" help="@HELP@"/>
    </xml>
    <xml name="min_reads2" token_help="Minimum number (default: 2) of variant-supporting reads at a position required to make a call">
        <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
            label="Minimum supporting reads" help="@HELP@"/>
    </xml>
    <xml name="min_avg_qual">
        <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
            label="Minimum base quality"
            help="The minimum base quality at the variant position required to use a read for calling" />
    </xml>
    <xml name="min_var_freq" token_value="0.01">
        <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
            label="Minimum variant allele frequency"
            help="Minimum variant allele frequency (default: @VALUE@) required for calling a variant"/>
    </xml>
    <xml name="min_freq_for_hom">
        <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
            label="Minimum homozygous variant allele frequency"
            help="Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype" />
    </xml>
    <xml name="p_value" token_value="0.01"
    token_label="p-value threshold for calling variants"
    token_help="">
        <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1"
            label="@LABEL@" help="@HELP@"/>
    </xml>
    <xml name="strand_filter">
        <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
            <option value="no" selected="True">no</option>
            <option value="yes">yes</option>
        </param>
    </xml>

    <token name="@HELP_HEADER@"><![CDATA[
**VarScan Overview**

VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_.

.. _VarScan: http://dkoboldt.github.io/varscan/
.. _here: http://dkoboldt.github.io/varscan/using-varscan.html
   ]]></token>
</macros>