annotate hictk.xml @ 5:af0d9df0641e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 92a0b58278588671dc47bceeef84bad41c429ed0

<tool id="hictk" name="hictk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>convert cool to juicebox hic</description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement version="@TOOL_VERSION@" type="package">hictk</requirement>
    </requirements>
    <version_command><![CDATA[echo "@TOOL_VERSION@"]]></version_command>
    <command><![CDATA[
      hictk convert -f --output-fmt 'hic' '$incool' '$outhic'
    ]]></command>
    <inputs>
        <param name="incool" type="data" format="cool,mcool,scool" label="cool/hdf5 data to convert to hic binary" />
    </inputs>
    <outputs>
        <data name="outhic" format="juicebox_hic" label="hictk convert on $incool.element_identifier hic" hidden="false"/>
    </outputs>
    <tests>
        <test>
            <param name="incool" value="incool_sample"/>
            <output name="outhic" value="outhic_sample" compare="sim_size" delta_frac="0.1" ftype="juicebox_hic" />
        </test>
    </tests>
    <help><![CDATA[
 This tool converts cool/mcool/scool format files into hic binary files

 **hictk**

 hictk is a blazing fast toolkit to work with .hic and .cool files.

 This repository hosts `hictk`: a set of CLI tools to work with Cooler, as well as `libhictk`: the C++ library underlying `hictk`.

 hictk_ is capable of reading files in `.cool`, `.mcool`, `.scool` and `.juicebox_hic` format (including hic v9) as well as writing `.cool` and `.mcool` files
 but this tool only writes `juicebox_hic` at present.

.. _hictk: https://github.com/paulsengroup/hictk

  ]]></help>
    <citations>
    <citation type="bibtex">@article{hictk,
author = {Roberto Rossini},
year = {2023},
url = {https://github.com/paulsengroup/hictk},
title = {hictk: blazing fast toolkit to work with .hic and .cool files}
}</citation>
    <citation type="doi">10.1093/bioinformatics/bts573</citation>
  </citations>
</tool>