--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/SpatialConstraintDefiner.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,60 @@
+<?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: [Docking]-->
+<tool id="SpatialConstraintDefiner" name="SpatialConstraintDefiner" version="1.1.0">
+  <description>define spatial constraint</description>
+  <macros>
+    <token name="@EXECUTABLE@">SpatialConstraintDefiner</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SpatialConstraintDefiner
+
+#if $param_option:
+  -option $param_option
+#end if
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_type:
+  -type
+  #if " " in str($param_type):
+    "$param_type"
+  #else
+    $param_type
+  #end if
+#end if
+#if $param_n:
+  -n $param_n
+#end if
+#if $param_p:
+  -p $param_p
+#end if
+</command>
+  <inputs>
+    <param name="param_option" type="data" format="ini" optional="True" value="0" label="input configuration file" help="(-option) "/>
+    <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 molecule file" help="(-i) "/>
+    <param name="param_type" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'fraction' or 'number' of compound atoms" help="(-type) ">
+      <option value="fraction">fraction</option>
+      <option value=" number"> number</option>
+    </param>
+    <param name="param_n" type="float" value="0.0" label="desired number/fraction of atoms in spatial area" help="(-n) "/>
+    <param name="param_p" type="float" value="0.0" label="penalty value" help="(-p) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="ini"/>
+  </outputs>
+  <help>This tool allows to define spatial constraints for docking or scoring.
+
+For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
+Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
+
+Output of this tool is a ini-file that contains the desired spatial constraint.
+
+</help>
+</tool>