comparison varscan_mpileup.xml @ 2:d062703d6f13 draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c

1:0bc800d67a0e

<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0">
    <description>for variant detection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
        ## Set up samples list file.
        #if $sample_names.strip() != '':
           echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&

            <param name="sample_names" value="" />
            <output name="output" file="varscan_mpileup_result1.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 detects variants from pileups.

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

**Input**

::

**Output**

VarScan produces a VCF 4.1 dataset as output.

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

2:d062703d6f13

<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.1">
    <description>for variant detection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.2.1">gawk</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
        ## Set up samples list file.
        #if $sample_names.strip() != '':
           echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&

            <param name="sample_names" value="" />
            <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" />
        </test>
    </tests>

    <help><![CDATA[
@HELP_HEADER@

**Input**

::

**Output**

VarScan produces a VCF 4.1 dataset as output.

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