--- a/CADDSuite-1.6/galaxyconfigs/tools/PocketCutter.xml	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-
-<!--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="1.6">
-    <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>
\ No newline at end of file