<!--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="0.94">
    <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" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
        <param name="org" label="molecule file containing the original ('true') poses" optional="false" 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>