<tool id="ucsc_nettoaxt" name="netToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Convert net (and chain) to axt format
    </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-nettoaxt</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    netToAxt
        '$in_net'
        '$in_chain'
        '$in_target'
        '$in_query'
        '$out'
        $qChain
        #if str($maxGap)
            -maxGap=$maxGap
        #end if
        $noSplit
    ]]></command>
    <inputs>
        <param name="in_net" format="ucsc.net" type="data" label="Net dataset" />
        <param name="in_chain" format="chain" type="data" label="Chain dataset" />
        <param name="in_target" format="twobit" type="data" label="Dataset with target sequence" />
        <param name="in_query" format="twobit" type="data" label="Dataset with query sequence" />
        <param argument="-qChain" type="boolean" optional="true" truevalue="-qChain" falsevalue="" label="Is the net with respect to the query side of chains?" />
        <param argument="-maxGap" type="integer" optional="true" min="0" label="Maximum size of gap before breaking" help="default 100" />
        <param argument="-noSplit" type="boolean" optional="true" truevalue="-noSplit" falsevalue="" label="Don't split chain when there is an insertion of another chain" />

    </inputs>
    <outputs>
        <data name="out" format="axt" />
    </outputs>
    <tests>
        <test>
            <param name="in_net" value="hg38.chrM.mm39.chrM.ucsc.net" />
            <param name="in_chain" value="hg38.chrM.mm39.chrM.chain" />
            <param name="in_target" value="hg38.chrM.twobit" />
            <param name="in_query" value="mm39.chrM.twobit" />
            <output name="out" file="out.axt" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`netToAxt`_ is a tool from the UCSC suite to convert dataset from `ucsc.net`_ format (and `alignment chains`_) to `axt`_ format.

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

.. _netToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
.. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
.. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netToAxt/netToAxt.c
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>