<tool id="roary_plots" name="Roary plots" version="1.0">
  <description>Generate plots from Roary outputs</description>
  <requirements>
	 <requirement type="package" version="1.78">biopython</requirement>
	 <requirement type="package" version="3.4.2">matplotlib</requirement>
	 <requirement type="package" version="1.20.2">numpy</requirement>
	 <requirement type="package" version="1.2.4">pandas</requirement>
	 <requirement type="package" version="0.11.1">seaborn</requirement>
</requirements>

<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="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="Pangenome matrix tree"/>
	 <data format="png" name="frequency" label="Pangenome frequency"/>
	 <data format="png" name="pie" label="Pangenome pie"/>
</outputs>

  <help>
 For full documentation, please go to the Roary plots website : https://github.com/sanger-pathogens/Roary/tree/master/contrib/roary_plots 
	  
</help>

</tool>