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

Uploaded
author marcel
date Tue, 12 Jul 2011 10:53:07 -0400
parents
children af446ca2d5c6
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Tue Jul 12 10:53:07 2011 -0400
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+
+<!--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="rmsdcalculator" name="RMSDCalculator" version="0.95">
+    <description>calculate RMSD between poses</description>
+    <command interpreter="bash"><![CDATA[../../RMSDCalculator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $org ) != ''  and str( $org ) != 'None' :
+   -org "$org"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet 
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="org" optional="false" label="molecule file containing the original ('true') poses" type="data" format="mol2/sdf/drf"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool calculates the RMSD between different conformations of the same molecule.
+
+Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
+Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
+
+Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
+</tool>
\ No newline at end of file
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