view chainsort.xml @ 1:5815f5bd9ac8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort commit 303002db06287fb25306020c4391626842f52162

<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.

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

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