<tool id="samtools_sort" name="Sort" version="2.0.1">
    <description>order of storing aligned sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        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>
    <tests>
        <test>
            <param name="input1" value="1.bam" ftype="bam" />
            <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
        </test>
        <test>
            <param name="input1" value="1.bam" ftype="bam" />
            <param name="sort_mode" value="-n"/>
            <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
        </test>
    </tests>
    <help>
**What it does**

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