<tool id="ucsc_chainsort" name="chainSort" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Sort chains
    </description>
    <macros>
        <token name="@TOOL_VERSION@">455</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-chainsort</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    chainSort
        '$in_chain'
        $sort_by
        '$out'
    ]]></command>
    <inputs>
        <param name="in_chain" format="chain" type="data" label="Chain dataset" />
        <param name="sort_by" type="select" label="Sort">
            <option value="" selected="true">by score</option>
            <option value="-target">on target start</option>
            <option value="-query">on query start</option>
        </param>
    </inputs>
    <outputs>
        <data name="out" format="chain" />
    </outputs>
    <tests>
        <test>
            <param name="in_chain" value="input.chain" />
            <output name="out" file="sorted_score.chain" />
        </test>
        <test>
            <param name="in_chain" value="input.chain" />
            <param name="sort_by" value="-query" />
            <output name="out" file="sorted_query.chain" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`chainSort`_ is a tool to sort chains.

Note this tool loads all chains into memory, so it is not suitable for large datasets. Instead, run chainSort on multiple small dataset, followed by chainMergeSort.

.. _chainSort: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>