--- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Tue Jul 12 10:29:49 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Fri Sep 02 08:48:21 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--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="ligcheck" name="LigCheck" version="0.95">
+<tool id="ligcheck" name="LigCheck" version="0.9.6">
     <description>check molecules for errors</description>
     <command interpreter="bash"><![CDATA[../../LigCheck 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -18,13 +18,21 @@
 #if str( $ut ) != ''  and str( $ut ) != 'None' :
    -ut
 #end if
+#if str( $nc ) != ''  and str( $nc ) != 'None' :
+   -nc
+#end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
         <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
         <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/>
         <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/>
-        <param name="ut" optional="true" label="check for unique topologies (default: check only for unique conformation)" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>