--- a/CADDSuite-1.6/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Sat Dec 15 13:10:41 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="1.6">
-    <description>define spatial constraint</description>
-    <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $type ) != ''  and str( $type ) != 'None' :
-   -type "$type"
-#end if
-#if str( $n ) != ''  and str( $n ) != 'None' :
-   -n "$n"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
-        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
-        <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select">
-            <option value="fraction">fraction</option>
-            <option value="number">number</option>
-        </param>
-        <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/>
-        <param name="p" optional="true" label="Optional: penalty value" type="text" area="true" size="1x5" value="5e11"/>
-    </inputs>
-    <outputs>
-        <data name="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>
\ No newline at end of file