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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="0.95">
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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 | tail -n 5
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34 ]]></command>
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35 <inputs>
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36 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
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37 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
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38 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
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39 <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/>
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40 <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="data"/>
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41 <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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42 <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select">
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43 <option value="Rescoring3D">Rescoring3D</option>
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44 <option value="Rescoring4D">Rescoring4D</option>
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45 <option value="Rescoring1D">Rescoring1D</option>
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46 </param>
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47 <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select">
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48 <option value="MM">MM</option>
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49 <option value="PLP">PLP</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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54 </outputs>
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55 <help>This tool rescores docking output poses using Target-specific Grid-Rescoring.
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56 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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57 As input TaGRes needs:
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58
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59 * a file containing a protonated protein in pdb-format
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60 * 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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61 * 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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62 * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
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63
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64 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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65
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66 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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67 </tool> |