Mercurial > repos > greg > gregs_test_repo
comparison CADDSuite-1.0.1/galaxyconfigs/tools/RMSDCalculator.xml @ 23:389056b8864a
Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
| author | greg |
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| date | Mon, 14 Nov 2011 17:02:30 -0500 |
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| 22:2615b9ede2c4 | 23:389056b8864a |
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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="1.0.1"> | |
| 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" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> | |
| 20 <param name="org" optional="false" label="molecule file containing the original ('true') poses" 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> |