diff CADDSuite/galaxyconfigs/tools/ProteinCheck.xml @ 3:bb26168c5715

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,34 @@
+
+<!--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="0.95">
+    <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>
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