<tool id="ucsc_netsyntenic" name="netSyntenic" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Add synteny info to a net
    </description>
    <macros>
        <token name="@TOOL_VERSION@">469</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-netsyntenic</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    netSyntenic
        '$in_net'
        '$out'
    ]]></command>
    <inputs>
        <param name="in_net" format="ucsc.net" type="data" label="Input net" />
    </inputs>
    <outputs>
        <data name="out" format="ucsc.net" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="in_net" value="input1.ucsc.net" />
            <output name="out" file="out1.ucsc.net"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`netSyntenic`_ is a tool to add synteny info to a net. See details of `net format`_.

For implementation details see netSyntenic's `source code`_.

.. _netSyntenic: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _net format: https://genome.ucsc.edu/goldenPath/help/net.html
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netSyntenic/netSyntenic.c
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>