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annotate CADDSuite-1.5/galaxyconfigs/tools/InteractionConstraintDefiner.xml @ 15:ac342506cd4e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -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="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="1.5">
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4 <description>define interaction constraint</description>
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5 <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner
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6 #if str( $res ) != '' and str( $res ) != 'None' :
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7 -res "$res"
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8 #end if
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9 #if str( $ini ) != '' and str( $ini ) != 'None' :
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10 -ini "$ini"
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11 #end if
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12 #if str( $s ) != '' and str( $s ) != 'None' :
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13 -s "$s"
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14 #end if
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15 #if str( $p ) != '' and str( $p ) != 'None' :
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16 -p "$p"
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17 #end if
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18 #if str( $o ) != '' and str( $o ) != 'None' :
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19 -o "$o"
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20 #end if
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21 | tail -n 5
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22 ]]></command>
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23 <inputs>
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24 <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
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25 <param name="res" optional="false" label="residue ID" area="true" type="text" size="1x15"/>
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26 <param name="s" optional="false" label="desired minimal interation (score) between ligand and specified residue(s)" type="text" area="true" size="1x5" value="-2.0"/>
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27 <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="10"/>
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28 </inputs>
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29 <outputs>
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30 <data name="o" format="ini"/>
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31 </outputs>
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32 <help>This tool allows to define interaction constraints for docking or scoring.
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34 The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: &lt;chain-ID&gt;:&lt;residue-ID&gt;, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
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36 Output of this tool is a ini-file that contains the desired interaction constraint.</help>
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37 </tool>