--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/Ligand3DGenerator.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,70 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Preparation]-->
+<tool id="Ligand3DGenerator" name="Ligand3DGenerator" version="1.1.0">
+  <description>generate 3D coordinates for small molecules</description>
+  <macros>
+    <token name="@EXECUTABLE@">Ligand3DGenerator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>Ligand3DGenerator
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_ph:
+  -ph $param_ph
+#end if
+#if $param_ff:
+  -ff     "$param_ff"
+#end if
+#if $param_rm:
+  -rm $param_rm
+#end if
+#if $param_k:
+  -k $param_k
+#end if
+#if $param_kp:
+  -kp $param_kp
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
+    <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/>
+    <param name="param_ff" type="text" size="30" value="MMFF94" label="Forcefield to use for optimization (any available OpenBabel plugin)" help="(-ff) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
+    <param name="param_k" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates (flag precedes '-kp')" help="(-k) "/>
+    <param name="param_kp" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates but re-protonate compound in a pH dependent manner (flag is preceded by '-k')" help="(-kp) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" metadata_source="param_i" format="input"/>
+  </outputs>
+  <help>This tool takes input molecules and generates a single 3D conformation which is ready for docking. The input has to be a chemical file
+containing valid topologies and conistent bond order assignements. 2D coordinates in the input file are overwritten, 3D coordinates can be kept ('-k' or '-kp').
+
+  '-k':   3D coordinates are tried to be kept. Molecules with non-zero coordinates in all three dimensions are passed through without modifications. 
+          However, if a molecule is not ready for docking (i.e. unusual bond leghts, unusual charges), the molecule will be rebuild and new 
+          3D coordinates are assigned. If only hydrogens are missing, the coordinates of non-hydrogen atoms are kept but the molecule gets newly protonated.
+  '-kp':  3D coordinates are tried to be kept as for the '-k' flag but the molecule will be newly protonated.
+
+Please note that the main purpose of this tool is to generate valid starting conformations for docking or other optimization procedures.
+Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) 
+different fragments might still overlap with each other.
+
+Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz.
+
+</help>
+</tool>