<tool id="samtools_sort" name="sort" version="1.0.2">
    <requirements>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <description>a BAM file</description>
    <command>
        samtools sort
            $sort_mode
            "${input1}" foo
            2&gt;&amp;1 || echo "Error running samtools sort." &gt;&amp;2
            ;
            mv foo.bam "${output1}"
    </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</option>
        </param>
    </inputs>
    <outputs>
        <data name="output1" format="bam" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bam" ftype="bam" />
            <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
        </test>
    </tests>
    <help>

**What it does**

This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.

.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml

------

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

    </help>
</tool>