--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/autodocktools_rec_plidflow.xml	Tue Jan 14 07:52:48 2020 -0500
@@ -0,0 +1,22 @@
+<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>