comparison netchainsubset.xml @ 0:6d5ab8d81db2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35

0:6d5ab8d81db2

<tool id="ucsc_netchainsubset" name="netChainSubset" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Create chain file with subset of chains that appear in the net
    </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-netchainsubset</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    netChainSubset
        '$in_net'
        '$in_chain'
        '$out'
        $splitOnInsert
        $wholeChains
        $skipMissing
    ]]></command>
    <inputs>
        <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" />
        <param name="in_chain" format="chain" type="data" label="chain dataset" help="" />
        <param argument="-splitOnInsert" type="boolean" optional="true" truevalue="-splitOnInsert" falsevalue="" label="Split on insert" help="Split chain when get an insertion of another chain." />
        <param argument="-wholeChains" type="boolean" optional="true" truevalue="-wholeChains" falsevalue="" label="Whole chains" help="Write entire chain references by net, don't split when a high-level net is encoundered.  This is useful when nets have been filtered." />
        <param argument="-skipMissing" type="boolean" optional="true" truevalue="-skipMissing" falsevalue="" label="Skip missing chains" help="Skip chains that are not found instead of generating an error. Useful if chains have been filtered." />
    </inputs>
    <outputs>
        <data name="out" format="chain" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="in_net" value="target.net" />
            <param name="in_chain" value="in.chain" />
            <output name="out" file="out.chain" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`netChainSubset`_ is a tool to create a `chain`_ file with subset of chains that appear in the net.
This process creates so called `liftOver`_ file used to convert coordinates between asesemblies.

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

.. _netChainSubset: https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER
.. _net: https://genome.ucsc.edu/goldenPath/help/net.html
.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
.. _liftOver: https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Liftover
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/151a59e4e7526124ff096019c6c4052f0a900711/src/hg/mouseStuff/netChainSubset/netChainSubset.c
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>