--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.6/galaxyconfigs/tools/SimilarityAnalyzer.xml	Sat Dec 15 13:15:46 2012 -0500
@@ -0,0 +1,35 @@
+
+<!--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="similarityanalyzer" name="SimilarityAnalyzer" version="1.6">
+    <description>analyze similarity between molecule files</description>
+    <command interpreter="bash"><![CDATA[../../SimilarityAnalyzer 
+#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
+   -i1 "$i1"
+#end if
+#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
+   -i2 "$i2"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $title ) != ''  and str( $title ) != 'None' :
+   -title "$title"
+#end if
+-quiet 
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i1" optional="false" label="input molecule file 1" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" optional="false" label="input molecule file 2" type="data" format="mol2/sdf/drf"/>
+        <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.
+
+Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.</help>
+</tool>
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