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annotate CADDSuite-1.5/galaxyconfigs/tools/IMGDock.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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1
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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="imeedydock" name="IMGDock" version="1.5">
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4 <description>Iterative Multi-Greedy Docking</description>
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5 <command interpreter="bash"><![CDATA[../../IMGDock
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6 #if str( $rec ) != '' and str( $rec ) != 'None' :
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7 -rec "$rec"
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8 #end if
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9 #if str( $rl ) != '' and str( $rl ) != 'None' :
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10 -rl "$rl"
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11 #end if
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12 #if str( $ini ) != '' and str( $ini ) != 'None' :
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13 -ini "$ini"
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14 #end if
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15 #if str( $i ) != '' and str( $i ) != 'None' :
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16 -i "$i"
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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 #if str( $grd ) != '' and str( $grd ) != 'None' :
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22 -grd "$grd"
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23 #end if
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24 #if str( $rm ) != '' and str( $rm ) != 'None' :
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25 -rm
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26 #end if
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27 | tail -n 5
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28 ]]></command>
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29 <inputs>
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30 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
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31 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
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32 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
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33 <param name="i" optional="false" label="compounds to be docked" type="data" format="mol2/sdf/drf"/>
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34 <param name="grd" optional="false" label="ScoreGrid file" type="data" format="grd.gz"/>
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35 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
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36 </inputs>
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37 <outputs>
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38 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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39 </outputs>
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40 <help>IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
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41 As input we need:
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42
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43 * a file containing a protonated protein in pdb-format
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44 * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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45 * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here.
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46 * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck.
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48 Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound.
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49
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50 Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.</help>
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51 </tool>