# HG changeset patch
# User bgruening
# Date 1719906979 0
# Node ID 2ca594a0caf7addcd3005bcebc61475fed529652

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e

diff -r 000000000000 -r 2ca594a0caf7 hictk.xml
--- /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>
diff -r 000000000000 -r 2ca594a0caf7 test-data/incool_sample
Binary file test-data/incool_sample has changed
diff -r 000000000000 -r 2ca594a0caf7 test-data/outhic_sample
Binary file test-data/outhic_sample has changed