Add juicebox_hic format and citation (#1383)

* 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...

* add citation and link to github
add juicebox_hic as the name of the output

* fix branch again

tools/hictk/hictk.xml

@@ -32,10 +32,19 @@
 
  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.
+ 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="doi">10.1093/bioinformatics/bts573</citation>
-    </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>