--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ob_prepare_ligands.xml	Fri May 10 08:55:09 2019 -0400
@@ -0,0 +1,86 @@
+<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@VERSION@.0">
+    <description>Tool to prepare ligands for docking with tools like Autodock Vina</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+	    mkdir output && obabel -i '${ligands.ext}' -o '$oformat' -O 'output/molecule.$oformat' -m '$ligands' $gen3d -p $ph_value
+    ]]></command>
+    <inputs>
+        <param type="data" name="ligands" format="sdf,mol2,inchi,smi" label="The ligands which need to be prepared" help="Input in SDF, MOL2, InChi or SMILES format." />
+        <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
+        <param name="gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
+        <param name="oformat" type="select" label="Output format" >
+            <option value="pdb">PDB</option>
+            <option value="pdbqt">PDBQT</option>
+            <option value="mol">MOL</option>
+            <option value="mol2">MOL2</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="file_outputs" type="list" label="Prepared ligands" >
+			<discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
+            <param name="oformat" value="pdbqt"/>
+            <param name="ph_value" value="7.4"/>
+            <output_collection name="file_outputs" type="list" count="10">
+                <element name="molecule1" file="ob_prepare_ligands1.pdbqt" />
+                <element name="molecule2" file="ob_prepare_ligands2.pdbqt" />
+                <!-- we check only the first 2 -->
+            </output_collection>
+        </test>
+        <test>
+            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
+            <param name="oformat" value="mol2"/>
+            <param name="ph_value" value="7.4"/>
+            <output_collection name="file_outputs" type="list" count="10">
+                <element name="molecule1" file="ob_prepare_ligands1.mol2" />
+                <element name="molecule2" file="ob_prepare_ligands2.mol2" />
+                <!-- we check only the first 2 -->
+            </output_collection>
+        </test>
+        <test>
+            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
+            <param name="oformat" value="mol"/>
+            <param name="ph_value" value="7.4"/>
+            <output_collection name="file_outputs" type="list" count="10">
+                <!-- just check the count -->
+            </output_collection>
+        </test>
+        <test>
+            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
+            <param name="oformat" value="pdb"/>
+            <param name="ph_value" value="7.4"/>
+            <output_collection name="file_outputs" type="list" count="10">
+                <!-- just check the count -->
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does?**
+
+This tool uses OpenBabel to convert an input molecule file, typically a SD file, to individual output molecule files in pdbqt, pdb, 
+mol or mol2 formats. There is one output file for each record in the input.
+Protonation is performed at a specified pH and 3D coordinates can optionally be generated. 3D coordinate generation should be used when 
+the docking program requires 3D structures and the input is not 3D.
+
+The most typical usage is to process a set of ligands in a SD file that will be docked by VINA. In this case the pdbqt output format should
+be used, and the resulting collection of molecules can be used as input by VINA.
+
+**Input**
+
+Molecules such as an SD file dataset in history.
+
+**Output**
+
+A collection of individual molecule files in the specified format.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+