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<tool id="varscan_pileup" name="VarScan pileup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>for variant detection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
varscan ${cmd} '${input}'
--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}
--p-value ${p_value}
--output-vcf 1 > '$output'
    ]]></command>
    <inputs>
        <param name="input" format="pileup" type="data" label="Samtools pileup file"/>
        <param name="cmd" type="select" label="Analysis type">
          <option value="pileup2snp" selected="True">Identify SNPs from a pileup file</option>
          <option value="pileup2indel">Identify indels a pileup file</option>
          <option value="pileup2cns">Call consensus and variants from a pileup file</option>
        </param>
        <param argument="--min-coverage" type="integer" value="8" min="1" max="200" label="Minimum coverage"/>
        <param argument="--min-reads2" type="integer" value="2" min="1" max="200" label="Minimum supporting reads"/>
        <param argument="--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"/>
        <param argument="--min-var-freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency" help="Minimum variant allele frequency required for calling a variant"/>
        <param argument="--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"/>
        <param argument="--p-value" type="float" value="0.01" min="0" max="1" label="Default p-value threshold for calling variants"/>
    </inputs>
    <outputs>
        <data name="output" format="vcf"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input1.pileup"/>
            <param name="cmd" value="pileup2snp"/>
            <param name="min_coverage" value="15"/>
            <param name="min_avg_qual" value="15"/>
            <param name="min_var_freq" value="0.8"/>
            <param name="p_value" value="0.01"/>
            <output name="output" file="output1.vcf" ftype="vcf"/>
        </test>
    </tests>

    <help><![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

**Input**

::

  pileup file - The SAMtools pileup file
 
**Output**

VarScan produces a VCF dataset as output.
    ]]></help>
    <expand macro="citations"/>
</tool>