view samtools_sort.xml @ 9:33ed69baef65 draft default tip

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<tool id="samtools_sort" name="Sort" version="0.1">
    <description>BAM dataset</description>
    <requirements>
        <requirement type="package" version="0.1">docker_samtools</requirement>
        <container type="docker">viv1/samtools:1.2</container>
    </requirements>
    <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
    <inputs>
        <param name="input1" type="data" format="bam" label="BAM File" />
        <param name="sort_mode" type="select" label="Sort by ">
            <option value="" selected="True">Chromosomal coordinates</option>
            <option value="-n">Read names (-n)</option>
        </param>
    </inputs>
    <outputs>
        <data name="output1" format="bam" />
    </outputs>
    <help>

**What it does**

This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
    </help>
</tool>