move panaroo to iuc repo

tools/panaroo/.shed.yml

@@ -0,0 +1,10 @@
+name: panaroo
+owner: galaxy-australia
+categories:
+- Pangenome
+description: A Bacterial Pangenome Analysis Pipeline
+homepage_url: https://gthlab.au/panaroo/#/
+long_description: |
+  a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies.
+remote_repository_url: https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo 
+type: unrestricted

tools/panaroo/macros.xml

@@ -0,0 +1,68 @@
+<macros>
+	<token name="@TOOL_VERSION@">1.5.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+	<token name="@PROFILE@">22.05</token>
+	<xml name="edam_ontology">
+	  <edam_topics>
+	     <edam_topic>topic_0194</edam_topic>
+     	  </edam_topics>
+  	</xml>
+        <xml name="biotools">
+            <xrefs>
+               <xref type="bio.tools">panaroo</xref>
+            </xrefs>
+    	</xml>
+	<xml name="requirements">
+           <requirements>
+	       <requirement type="package" version="@TOOL_VERSION@">panaroo</requirement>
+	       <requirement type="package" version="170427">prank</requirement>	
+    	   </requirements>
+        </xml>
+        <xml name="clean_mode">
+            <option value="strict">strict</option>
+	    <option value="moderate">moderate</option>
+	    <option value="sensitive">sensitive</option>
+    	</xml>
+	<xml name="genetic_code">
+             <option value="1">1. Standard</option>
+             <option value="2">2. Vertebrate Mitochondrial</option>
+             <option value="3">3. Yeast Mitochondrial</option>
+	     <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
+             <option value="5">5. Invertebrate Mitochondrial</option>
+             <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
+             <option value="9">9. Echinoderm Mitochondrial</option>
+             <option value="10">10. Euplotid Nuclear</option>
+             <option value="11" selected="True">11. Bacteria and Archaea</option>
+             <option value="12">12. Alternative Yeast Nuclear</option>
+             <option value="13">13. Ascidian Mitochondrial</option>
+             <option value="14">14. Flatworm Mitochondrial</option>
+             <option value="15">15. Blepharisma Macronuclear</option>
+             <option value="16">16. Chlorophycean Mitochondrial</option>
+             <option value="21">21. Trematode Mitochondrial</option>
+             <option value="22">22. Scenedesmus obliquus mitochondrial</option>
+             <option value="23">23. Thraustochytrium Mitochondrial</option>
+	     <option value="24">24. Pterobranchia mitochondrial</option>
+	     <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
+	     <option value="26">26. Pachysolen tannophilus Nuclear Code</option>
+	     <option value="27">27. Karyorelict Nuclear Code</option>
+	     <option value="28">28. Condylostoma Nuclear Code</option>
+	     <option value="29">29. Mesodinium Nuclear Code</option>
+	     <option value="30">30. Peritrich Nuclear Code</option>
+	     <option value="31">31. Blastocrithidia Nuclear Code</option>
+	     <option value="33">33. Cephalodiscidae Mitochondrial UAA-Tyr Code</option>
+     	</xml>
+	<xml name="refind_mode_option">
+	   <option value="default" selected="True">default</option>
+	   <option value="strict">strict</option>
+	   <option value="off">off</option>
+	</xml>
+	<xml name="gene_alignment">
+	    <option value="None" selected="True">None</option>
+	    <option value="core">core</option>
+	    <option value="pan">pan</option>
+    	</xml>
+	<xml name="gene_aligner">
+	    <option value="mafft" selected="True">mafft</option>
+	    <option value="prank">prank</option>
+	</xml>
+</macros>