<tool id="autodocktools_receptor_plidflow" name="PLIDflow: AutoDock Receptor">
  <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="receptor_pdb" type="data" format="pdb" label="Receptor PDB file" help="Preparing the receptor involves adding gasteiger charges and adding hydrogens. The formatted receptor is written in a 'pdbqt' file."/>
  </inputs>
  <command><![CDATA[
	 
	  swpath=\$(which prepare_receptor4.py) ; 
	  cp ${receptor_pdb} ${receptor_pdb}.pdb ; 
	  pythonsh \$swpath -r ${receptor_pdb}.pdb -A hydrogens -o $receptor_pdbqt;
	  rm ${receptor_pdb}.pdb; 
	  Rscript ${__tool_directory__}/scripts/pdbqtcorrector2step.R ${receptor_pdbqt} ${receptor_pdbqt_modified2} ${receptor_types};

	]]></command>

  <outputs>
	  <data name="receptor_pdbqt" format="pdbqt" label="Receptor PDBQT file"/>
	  <data name="receptor_pdbqt_modified" format="pdbqt" label="Receptor PDBQT file modified"/>
	  <data name="receptor_pdbqt_modified2" format="pdbqt" label="Receptor PDBQT file modified 2"/>
	  <data name="receptor_types" format="txt" label="Receptor types molecules"/>
  </outputs>
</tool>