diff PLIDflow/autodocktools_rec_plidflow.xml @ 6:795e11fac81b draft default tip

Included new tools for standardization
author bitlab
date Wed, 22 Apr 2020 06:12:00 -0400
parents 6fcfa4756040
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/autodocktools_rec_plidflow.xml	Wed Apr 22 06:12:00 2020 -0400
@@ -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>