<tool id="pdb2pqr_plidflow" name="PLIDflow: PDB2PQR">
  <description>Converts a pdb to pqr</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. First it will be processed by pdb2pqr."/>
  </inputs>
  <command><![CDATA[
	  swpath=\$(which pdb2pqr.py) ;

	  ${__tool_directory__}/scripts/preparePDB2PQR_plidflow.sh ${receptor_pdb} ${receptor_pdb}.prepdb ; 

	  (python2.7 \$swpath --ff=amber --ffout=amber --verbose --chain --ph-calc-method=propka --with-ph=7.0 --drop-water ${receptor_pdb}.prepdb ${pdb_processed}.pqr ) &> /dev/null ;

	  rm ${receptor_pdb}.prepdb ;
	  
	  ${__tool_directory__}/scripts/includeAtom3.sh ${__tool_directory__}/scripts/table ${pdb_processed}.pqr > ${pdb_processed}  ;
	  
	  rm ${pdb_processed}.pqr ;
  
	]]></command>
  <outputs>
	  <data name="pdb_processed" format="pdb" label="${receptor_pdb.name}_processed"/>
  </outputs>
</tool>