comparison varscan_copynumber.xml @ 1:8d8de66233ea draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177

0:a584f046e4a7

<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}

            --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"

    <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**

1:8d8de66233ea

<tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.1">
    <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
            @INPUT_PILEUPS@
            --min-coverage ${min_coverage}
            --min-base-qual ${min_base_qual}
            --min-map-qual ${min_map_qual}

            --min-segment-size ${min_segment_size}

            --data-ratio ${data_ratio}

    ]]></command>

    <inputs>
        <expand macro="input_pileups"/>

        <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"

    <outputs>
        <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>
    </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>
            <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" />
        </test>
        <test>
            <conditional name="pileup">
                <param name="pileup_select" value="combined" />
                <param name="combined_pileup" value="NT.pileup.gz" />
            </conditional>
            <output name="output" file="varscan_copynumber_result2.interval" lines_diff="0" />
        </test>
    </tests>

    <help>
**VarScan Overview**