--- a/CADDSuite-1.6/galaxyconfigs/tools/ProteinProtonator.xml	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +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="proteinprotonator" name="ProteinProtonator" version="1.6">
-    <description>protonate protein structures</description>
-    <command interpreter="bash"><![CDATA[../../ProteinProtonator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ph ) != ''  and str( $ph ) != 'None' :
-   -ph "$ph"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" optional="false" label="input file" type="data" format="pdb"/>
-        <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdb" format_source="i"/>
-    </outputs>
-    <help>ProteinProtonator allows you add hydrogens to a protein structure.
-
-Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
-
-Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help>
-</tool>
\ No newline at end of file