<tool id="autodocktools_ligand_plidflow" name="PLIDflow: AutoDock Ligand">
  <description>AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.</description>
  <inputs>
	  <param name="ligand_pdb" type="data" format="pdb" label="Ligand PDB file" help="The formatted receptor is written in a 'pdbqt' file."/>
  </inputs>
  <command><![CDATA[

	  swpath=\$(which prepare_ligand4.py) ; 
	  cp ${ligand_pdb} ${ligand_pdb}.pdb ; 
	  (pythonsh \$swpath -l ${ligand_pdb}.pdb -o $ligand_pdbqt) ;
	  rm ${ligand_pdb}.pdb ;

	 ]]></command>
  <outputs>
    <data name="ligand_pdbqt" format="pdbqt" label="Ligand PDBQT file"/>
  </outputs>
</tool>