<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1">
    <description>Call germline/somatic variants from tumor-normal pileups</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
        varscan somatic
            @INPUT_PILEUPS@
            --min-coverage ${min_coverage}
            --min-reads2 ${min_reads2}
            --min-avg-qual ${min_avg_qual}
            --min-var-freq ${min_var_freq}
            --min-freq-for-hom ${min_freq_for_hom}
            --normal-purity ${normal_purity}
            --tumor-purity ${tumor_purity}
            --tumor-purity ${tumor_purity}
            --min-coverage-normal ${min_coverage_normal}
            --somatic-p-value ${somatic_p_value}
            --p-value ${p_value}
            #if str($strand_filter) == 'yes':
              --strand-filter 1
            #end if

            --output-vcf 1
    ]]></command>

    <inputs>

        <expand macro="input_pileups"/>

        <expand macro="min_coverage" />
        <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200"
            label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" />
        <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200"
            label="Minimum read depth from the tumor sample" help="Minimum depth at a position to make a call" />
        <expand macro="min_reads2" />
        <expand macro="min_avg_qual" />
        <expand macro="min_var_freq" value="0.10" />
        <expand macro="min_freq_for_hom" />
        <param argument="--normal-purity" name="normal_purity" type="float" value="1.00" min="0" max="1.00"
            label="Estimated purity (non-tumor content) of normal sample"/>
        <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.00" min="0" max="1.00"
            label="Estimated purity (tumor content) of tumor sample"/>
        <expand macro="p_value" label="P-value threshold to call a heterozygote" value="0.99"/>
        <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
            label="p-value threshold for calling somatic sites"/>
        <expand macro="strand_filter" />
    </inputs>
    <outputs>
        <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/>
        <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/>
    </outputs>
    <tests>
        <test>
            <conditional name="pileup">
                <param name="pileup_select" value="separated" />
                <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
                <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
            </conditional>
            <param name="min_coverage" value="2" />
            <param name="min_coverage_normal" value="2" />
            <param name="min_coverage_tumor" value="2" />
            <param name="min_reads2" value="1" />
            <param name="min_avg_qual" value="5" />
            <param name="min_var_freq" value="0.01" />
            <param name="min_freq_for_hom" value="0.75" />
            <param name="normal_purity" value="0.6" />
            <param name="tumor_purity" value="0.6" />
            <param name="p_value" value="0.99" />
            <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" />
            <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" />
        </test>
        <test>
            <conditional name="pileup">
                <param name="pileup_select" value="combined" />
                <param name="combined_pileup" value="NT.pileup.gz" />
            </conditional>
            <param name="min_coverage" value="2" />
            <param name="min_coverage_normal" value="2" />
            <param name="min_coverage_tumor" value="2" />
            <param name="min_reads2" value="1" />
            <param name="min_avg_qual" value="5" />
            <param name="min_var_freq" value="0.01" />
            <param name="min_freq_for_hom" value="0.75" />
            <param name="normal_purity" value="0.6" />
            <param name="tumor_purity" value="0.6" />
            <param name="p_value" value="0.99" />
            <output name="output_indel" file="varscan_somatic_indel_result2.vcf" lines_diff="0" />
            <output name="output_snp" file="varscan_somatic_snp_result2.vcf" lines_diff="0" />
        </test>
    </tests>

    <help>
**VarScan Overview**

VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.

This tool calls germline/somatic variants from tumor-normal pileups.

.. _VarScan: http://dkoboldt.github.io/varscan/
.. _online: http://dkoboldt.github.io/varscan/using-varscan.html

**Input**

::

  mpileup file - The SAMtools mpileup files for the normal and tumor tissue
 

**Output**

VarScan produces a VCF 4.1 dataset as output.


    </help>
    <expand macro="citations" />
</tool>