annotate lumpyexpress.xml @ 6:d918a7f05d27 draft

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 1d3a527efa92cc763dc4aaabe1f7d1cc1651a444-dirty

<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.4">
    <description>Single or paired end SV detection</description>

    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package" version="0.8.3">pysam</requirement>
        <requirement type="package" version="1.13.1">numpy</requirement>
        <requirement type="package" version="0.2.13">lumpy-sv</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="0.1.24">samblaster</requirement>
        <requirement type="package" version="0.6.5">sambamba</requirement>
        <requirement type="package" version="4.2.1">gawk</requirement>
    </requirements>

    <version_command><![CDATA[
        lumpy 2>&1 >/dev/null | grep Program | cut -d ' ' -f 4 | cut -d ')' -f 1
    ]]></version_command>

    <command detect_errors="aggressive">
        <![CDATA[
            $__tool_directory__/lumpy_wrapper.tcsh
            '$paired'
            '$outfile'
            #for $bam in $bams
                '$bam'
            #end for
        ]]>
    </command>

    <inputs>
        <param format="bam"
               name="bams"
               label="Bam file(s)"
               argument="argument positions 3-N"

               type="data"
               multiple="true"

               help="Optionally sorted/indexed whole bam files.  Splitters and discordants will be extracted from this file."/>

        <param name="paired"
               label="Bam files contain paired end data"
               argument="argument position 1"

               type="boolean"
               truevalue="1"
               falsevalue="0"
               checked="no"
               value="false"/>
    </inputs>

    <outputs>
        <data format="vcf" name="outfile" />
    </outputs>

    <tests>
        <test>
            <param name="bams" value="test1-1.bam,test1-2.bam,test1-3.bam"/>
            <param name="paired" value="1"/>
            <output name="outfile" file="lumpy-test1.vcf"/>
        </test>
    </tests>

    <help>
        <![CDATA[
            Paired-end data is processed with lumpyexpress using only the required arguments.  Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`.  Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools

            Split reads and discordant reads are extracted from the supplied bam files.  Each bam file should represent a different sample.

            This is a wrapper for lumpyexpress that comes with lumpy-sv version 0.2.13.  The script in the latest version of lumpy-sv (0.2.14a) has some issues when run on galaxy.
        ]]>
    </help>

    <citations>
        <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
    </citations>

</tool>