<tool id="cluster_to_vina_cluster_plidflow" name="PLIDflow: Vina File Maker Multiple">
  <description>is a tool to select optimal Vina mode 1 energy.</description>
  <inputs>
    <param name="receptor_pdbqt" type="data" format="pdbqt" label="Receptor PDBQT file" help=""/>
    <param name="receptor_pdbqt_modified" type="data" format="pdbqt" label="Receptor PDBQT file modified" help=""/>
    <param name="receptor_pdbqt_modified2" type="data" format="pdbqt" label="Receptor PDBQT file modified 2" help=""/>
    <param name="ligand_pdbqt" type="data" format="pdbqt" label="Ligand PDBQT file" help=""/>
    <param name="size_x" type="data" format="txt" label="Grid size" help="eboxSize returns a single number that is the optimal edge length of a cubic docking box."/>

    <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."/>
    <param name="ligand_smi" type="data" format="smi" label="Drug SMI file" help="Open Babel is a chemical toolbox designed to speak the many languages of chemical data. To convert Line notation SMILES (Simplified Molecular Input Line Entry System) to coordinate data and bond matrix information in structure Data Format (SDF) format"/>
    <param name="receptor_types" type="data" format="txt" label="Receptor types" help="File containing the receptor types" />
    <param name="proteinCode" type="text" value="" label="Code for the protein (e.g. 3VRI)" help="In case the protein has already been computed, this will accelerate the binding process by several hours. Leave blank for no code."/>

  </inputs>
  <command><![CDATA[
	  nameX="${receptor_pdb.name}";
          nameY="${ligand_smi.name}";

	  nameX=\$(echo \${nameX//[^[:alnum:]]/_});

	  nameY=\$(echo \${nameY//[^[:alnum:]]/_});


	  ${__tool_directory__}/launch_confmaker_multiple.sh $receptor_pdbqt $receptor_pdbqt_modified $receptor_pdbqt_modified2 $ligand_pdbqt $size_x $out $log \$nameX \$nameY $receptor_pdb $receptor_types ${__tool_directory__} $proteinCode; 
  
	  ]]></command>
  <outputs>
	  <data name="out" format="zip" label="Output pdbqt from vina"/>
	  <data name="log" format="zip" label="Output log from vina"/>
  </outputs>
</tool>