Mercurial > repos > bgruening > hictk
changeset 0:2ca594a0caf7 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
| author | bgruening |
|---|---|
| date | Tue, 02 Jul 2024 07:56:19 +0000 |
| parents | |
| children | aaac573e899a |
| files | hictk.xml test-data/incool_sample test-data/outhic_sample |
| diffstat | 3 files changed, 50 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hictk.xml Tue Jul 02 07:56:19 2024 +0000 @@ -0,0 +1,50 @@ +<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@">1.0.0</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>