--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.5/galaxyconfigs/tools/PocketCutter.xml	Tue Jul 24 11:13:59 2012 -0400
@@ -0,0 +1,33 @@
+
+<!--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="pocketcutter" name="PocketCutter" version="1.5">
+    <description>cut binding pocket surface</description>
+    <command interpreter="bash"><![CDATA[../../PocketCutter 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="true" label="reference ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="input ini file" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf"/>
+    </outputs>
+    <help>This tools selects all atoms from a given protein structure that form part of the binding pocket's SES surface.
+
+The location and size of the binding pocket can be obtained from either a given reference ligand or an ini file that contains a description as generated by the PocketDetector tool, or both.
+
+The output of this tool is a molecule file that contain just the selected surface atoms and can be used e.g. with SurfaceMatcher.</help>
+</tool>
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