annotate chainswap.xml @ 0:6a7085c7777e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainswap commit b01ca34a85a25cf8fd38bdc005dc2e00d33a2d17

<tool id="ucsc_chainswap" name="chainSwap" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Swap target and query in a chain.
    </description>
    <macros>
        <token name="@TOOL_VERSION@">482</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-chainswap</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    chainSwap
        '$in_chain'
        '$out'
    ]]></command>
    <inputs>
        <param name="in_chain" format="chain" type="data" label="chain dataset" help="" />
    </inputs>
    <outputs>
        <data name="out" format="chain" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="in_chain" value="in.chain" />
            <output name="out" file="out.chain" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`chainSwap`_ is a tool to swap target with query in a `chain`_ file.

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

.. _chainSwap: https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER
.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/0d2aae0eda9aad8255bced9aa142e457f1a25c5d/src/hg/mouseStuff/chainSwap/chainSwap.c
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>