--- a/roary_plots.xml	Fri Nov 12 16:30:50 2021 +0000
+++ b/roary_plots.xml	Fri Nov 12 16:32:26 2021 +0000
@@ -8,18 +8,19 @@
 	 <requirement type="package" version="0.11.1">seaborn</requirement>
 </requirements>
 
-  <command interpreter="perl">roary_plots.sh $tree $input $heatmap
-</command>
+<command>${__tool_directory__}/Roary/contrib/roary_plots/roary_plots.py --labels $tree $input ;cp pangenome_matrix.png $heatmap; cp -rf pangenome_frequency.png $frequency; cp -rf pangenome_pie.png $pie</command>
 
  
   <inputs>
-  <param format="tabular" name="input" type="data" label="Gene Presence Absence matrix"/>
+  <param format="csv" name="input" type="data" label="Gene Presence Absence matrix"/>
   <param format="newick" name="tree" type="data" label="Newick"/>
    
  </inputs>
 
  <outputs>  
-	 <data format="png" name="heatmap" label="Heatmap tree"/>
+	 <data format="png" name="heatmap" label="Pangenome matrix tree"/>
+	 <data format="png" name="frequency" label="Pangenome frequency"/>
+	 <data format="png" name="pie" label="Pangenome pie"/>
 </outputs>
 
   <help>