Mercurial > repos > jbrayet > samtools_sort_docker

view samtools_sort.xml @ 8:b499934c6780 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jbrayet
date Wed, 18 Nov 2015 08:09:30 -0500
parents e95f34f52fc8
children 33ed69baef65
line wrap: on
line source

<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">samtools:1.0</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>