--- a/CADDSuite-1.6/galaxyconfigs/tools/RMSDCalculator.xml	Sat Dec 15 13:10:41 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +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="rmsdcalculator" name="RMSDCalculator" version="1.6">
-    <description>calculate RMSD between poses</description>
-    <command interpreter="bash"><![CDATA[../../RMSDCalculator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $org ) != ''  and str( $org ) != 'None' :
-   -org "$org"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
--quiet 
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
-        <param name="org" optional="false" label="molecule file containing the original ('true') poses" type="data" format="mol2/sdf/drf"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool calculates the RMSD between different conformations of the same molecule.
-
-Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
-Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
-
-Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
-</tool>
\ No newline at end of file