Mercurial > repos > marcel > caddsuite_linux_x86_64
annotate CADDSuite-1.5/galaxyconfigs/tools/TaGRes.xml @ 15:ac342506cd4e draft
CADDSuite version 1.5
author | Marcel Schumann <schumann.marcel@gmail.com> |
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date | Tue, 24 Jul 2012 11:08:49 -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="tagres" name="TaGRes" version="1.5"> |
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4 <description>Target-specific Grid-Rescoring</description> |
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5 <command interpreter="bash"><![CDATA[../../TaGRes |
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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( $mod ) != '' and str( $mod ) != 'None' : |
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19 -mod "$mod" |
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20 #end if |
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21 #if str( $tf ) != '' and str( $tf ) != 'None' : |
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22 -tf "$tf" |
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23 #end if |
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24 #if str( $o ) != '' and str( $o ) != 'None' : |
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25 -o "$o" |
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26 #end if |
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27 #if str( $method ) != '' and str( $method ) != 'None' : |
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28 -method "$method" |
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29 #end if |
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30 #if str( $function ) != '' and str( $function ) != 'None' : |
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31 -function "$function" |
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32 #end if |
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33 #if str( $rm ) != '' and str( $rm ) != 'None' : |
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34 -rm |
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35 #end if |
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36 | tail -n 5 |
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37 ]]></command> |
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38 <inputs> |
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39 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> |
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40 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> |
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41 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> |
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42 <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> |
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43 <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="mod"/> |
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44 <param name="tf" optional="true" label="Optional: top-scored fraction of compounds not to be rescored" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> |
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45 <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select"> |
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46 <option value="Rescoring3D">Rescoring3D</option> |
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47 <option value="Rescoring4D">Rescoring4D</option> |
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48 <option value="Rescoring1D">Rescoring1D</option> |
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49 </param> |
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50 <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select"> |
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51 <option value="MM">MM</option> |
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52 <option value="PLP">PLP</option> |
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53 </param> |
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54 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> |
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55 </inputs> |
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56 <outputs> |
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57 <data name="o" format="mol2/sdf/drf" format_source="i"/> |
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58 </outputs> |
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59 <help>This tool rescores docking output poses using Target-specific Grid-Rescoring. |
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60 Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool. |
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61 As input TaGRes needs: |
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62 |
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63 * a file containing a protonated protein in pdb-format |
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64 * 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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65 * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein. |
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66 * a regression model file as generated by TaGRes-train for same protein target than the one specified here. |
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67 |
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68 TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy. |
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69 |
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70 Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help> |
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71 </tool> |