--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.1/galaxyconfigs/tools/MolCombine.xml	Thu Jan 12 11:07:03 2012 -0500
@@ -0,0 +1,49 @@
+
+<!--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="molcombine" name="MolCombine" version="1.1">
+    <description>combine molecular files</description>
+    <command interpreter="bash"><![CDATA[../../MolCombine 
+#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
+   -i1 "$i1"
+#end if
+#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
+   -i2 "$i2"
+#end if
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ignH ) != ''  and str( $ignH ) != 'None' :
+   -ignH
+#end if
+#if str( $replace_prop ) != ''  and str( $replace_prop ) != 'None' :
+   -replace_prop
+#end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select">
+            <option value="intersection">intersection</option>
+            <option value="union">union</option>
+            <option value="b_not_a">b_not_a</option>
+        </param>
+        <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/>
+        <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i1"/>
+    </outputs>
+    <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
+
+If you want to match molecules regardless of their protonation state, use option '-ignH'.
+
+Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help>
+</tool>
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