--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.6/galaxyconfigs/tools/ProteinProtonator.xml	Sat Dec 15 13:15:46 2012 -0500
@@ -0,0 +1,29 @@
+
+<!--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>
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