Cool to hic (#1382)

* adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker
It actually does work. Sort of.
Hope this is useful to someone.

* fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :)

* add yara mapper ToolFactory - NOT from nf-core.
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

* small test files still work :)

* single quotes for $runme - disappeared mysteriously :(

* adding panaroo

* Finally fixed the '$runme' suggestion and got the sanitisers not to.

* fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement...

* cool_to_hic tool

* add cool_to_hic

* cleanup other branch

* fix bogus gfastats fix

* fix gfastats

* and again

* fix yaml

* fix so allows cool/mcool/scool - untested as I got no data...

* need test data.

* fixes from review

* fix bogus help transition

* Update .shed.yml

* some small cleanups

* Update .shed.yml

* lets call it juicebox_hic

---------

Co-authored-by: Björn Grüning <[email protected]>

tools/hictk/.shed.yml

@@ -0,0 +1,9 @@
+name: hictk
+owner: bgruening
+homepage_url: https://github.com/paulsengroup/hictk
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/hictk
+type: unrestricted
+category:
+- Convert Formats
+- Epigenetics
+description: hictk, a blazing-fast toolkit to work with .hic and .cool files

tools/hictk/hictk.xml

@@ -0,0 +1,41 @@
+<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@">0.0.8</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 `.hic` format (including hic v9) as well as writing `.cool` and `.mcool` files.
+
+  ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts573</citation>
+    </citations>
+</tool>