--- a/CADDSuite-1.6/galaxyconfigs/tools/ProteinCheck.xml	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +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="proteincheck" name="ProteinCheck" version="1.6">
-    <description>quality check for proteins structures</description>
-    <command interpreter="bash"><![CDATA[../../ProteinCheck 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $bc ) != ''  and str( $bc ) != 'None' :
-   -bc
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
-        <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdf"/>
-    </outputs>
-    <help>Check a given protein structure for the following errors:
-    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
-    * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
-    * each atom must have a valid assigned element
-    * the protein must be protonated (since this is necessary for docking/(re-)scoring).
-    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
-    * there may be no senseless temperature factors (&lt;1 or &gt;100)
-    * there may be no sterical clashes between atoms
-
-A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.</help>
-</tool>
\ No newline at end of file