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comparison CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml @ 0:8ce0411aaeb3

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Uploaded CADDSuite version 0.94
author marcel
date Sun, 26 Jun 2011 14:01:09 -0400
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1
2 <!--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.-->
3 <tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
4 <description>calculate RMSD between poses</description>
5 <command interpreter="bash"><![CDATA[../../RMSDCalculator
6 #if str( $i ) != '' and str( $i ) != 'None' :
7 -i "$i"
8 #end if
9 #if str( $org ) != '' and str( $org ) != 'None' :
10 -org "$org"
11 #end if
12 #if str( $o ) != '' and str( $o ) != 'None' :
13 -o "$o"
14 #end if
15 -quiet
16 | tail -n 5
17 ]]></command>
18 <inputs>
19 <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
20 <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/>
21 </inputs>
22 <outputs>
23 <data name="o" format="mol2/sdf/drf" format_source="i"/>
24 </outputs>
25 <help>This tool calculates the RMSD between different conformations of the same molecule.
26
27 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.
28 Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
29
30 Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
31 </tool>