<tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.0">
    <description>Determine relative tumor copy number from tumor-normal pileups</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[

        varscan copynumber
            '${normal_pileup}'
            '${tumor_pileup}'
            galaxy_out
            --min-coverage ${min_coverage}
            --min-base-qual ${min_base_qual}
            --min-map-qual ${min_map_qual}

            --min-segment-size ${min_segment_size}
            --max-segment-size ${max_segment_size}
            --p-value ${p_value}
            --data-ratio ${data_ratio}

    ]]></command>

    <inputs>
        <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
        <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>

        <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200"
            label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/>

        <param argument="--min-base-qual" name="min_base_qual" type="integer" value="20" min="1" max="200"
            label="Minimum base quality to count for coverage"/>
        <param argument="--min-map-qual" name="min_map_qual" type="integer" value="20" min="1" max="200"
            label="Minimum read mapping quality to count for coverage"/>

        <param argument="--min-segment-size" name="min_segment_size" type="integer" value="10" min="1" max="200"
            label="Minimum number of consecutive bases to report a segment" help="" />
        <param argument="--max-segment-size" name="max_segment_size" type="integer" value="100" min="1" max="200"
            label="Max size before a new segment is made" help="" />

        <expand macro="p_value" label="P-value threshold for significant copynumber change-point" value="0.01" />

        <param argument="--data-ratio" name="data_ratio" type="float" value="1.0" min="0.0" max="1.0"
            label="The normal/tumor input data ratio for copynumber adjustment"/>

        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>

    </inputs>
    <outputs>
        <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>
    </outputs>
    <tests>
        <test>
            <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
            <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
            <output name="output" file="varscan_copynumber_result1.interval" 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 estimates the relative tumor copy number 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>