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annotate CADDSuite-1.5/galaxyconfigs/tools/RMSDCalculator.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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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.-->
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3 <tool id="rmsdcalculator" name="RMSDCalculator" version="1.5">
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4 <description>calculate RMSD between poses</description>
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5 <command interpreter="bash"><![CDATA[../../RMSDCalculator
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $org ) != '' and str( $org ) != 'None' :
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10 -org "$org"
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11 #end if
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12 #if str( $o ) != '' and str( $o ) != 'None' :
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13 -o "$o"
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14 #end if
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15 -quiet
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16 | tail -n 5
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17 ]]></command>
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18 <inputs>
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19 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
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20 <param name="org" optional="false" label="molecule file containing the original ('true') poses" type="data" format="mol2/sdf/drf"/>
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21 </inputs>
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22 <outputs>
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23 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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24 </outputs>
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25 <help>This tool calculates the RMSD between different conformations of the same molecule.
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26
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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.
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28 Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
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29
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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>
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31 </tool>