New Tool Addition: PIRATE Tool (#7632)

* Add Pirate Tool

* Update category

* Cleanup

* Code changes as per review

* Update tools/pirate/pirate.xml

Co-authored-by: M Bernt <m.bernt@ufz.de>

* Update tools/pirate/pirate.xml

Co-authored-by: M Bernt <m.bernt@ufz.de>

* Update requirements

* Update requirements, add new test for plotting

* Minor reformatting

---------

Co-authored-by: M Bernt <m.bernt@ufz.de>

Author: SaimMomin12

tools/pirate/.shed.yml

@@ -0,0 +1,16 @@
+name: pirate
+owner: iuc
+categories:
+- Sequence Analysis
+- Genome annotation
+description: Pangenome Iterative Refinement and Threshold Evaluation.
+long_description: |
+  PIRATE is a comprehensive pangenomics toolbox for gene clustering and pangenome 
+  construction. It uses a range of identity thresholds to iteratively refine 
+  gene clusters, allowing for the identification of orthologs across diverse 
+  evolutionary scales and the classification of complex paralogous gene families.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate
+homepage_url: https://github.com/SionBayliss/PIRATE
+type: unrestricted
+maintainers:
+- SaimMomin12

tools/pirate/macros.xml

@@ -0,0 +1,25 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">pirate</requirement>
+        </requirements>
+    </xml>
+    <xrefs>
+        <xref type="bio.tools">PIRATE</xref>
+    </xrefs>
+    <xml name="creator">
+        <creator>
+            <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
+            <person givenName="Fernando" familyName="Martin Garcia" url="https://github.com/FMG0411"/>
+            <organization name="Galaxy Europe"/>
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/gigascience/giz119</citation>
+        </citations>
+    </xml>
+</macros>