--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,31 @@
+
+<!--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="0.94">
+    <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" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="org" label="molecule file containing the original ('true') poses" optional="false" 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>
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