<tool id="separate_chain_plidflow" name="PLIDflow: Separate Chains">
  <description>Separates chains from a PDB into multiple files</description>
  <inputs>
	  <param name="pdb" type="data" format="pdb" label="PDB file" help="PDB file to be separated into chains"/>
  </inputs>
  <command><![CDATA[
	  
	  ${__tool_directory__}/scripts/separateChain.sh ${pdb};
	  
  
	]]></command>
  <outputs>
	  <data name="Chains" format="pdb">
		       <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdb" format="pdb" directory="." visible="true" />
		  <!-- <discover_datasets pattern="(chain)([a-zA-Z0-9]+)[.](pdb)" format="pdb" directory="." visible="true" /> -->
          </data>
  </outputs>
</tool>