annotate CADDSuite/galaxyconfigs/tools/TaGRes-train.xml @ 3:ff6df146c0d5

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author marcel
date Sun, 26 Jun 2011 13:53:57 -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="tagres-train" name="TaGRes-train" version="0.94">
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4 <description>Target-specific Grid-Rescoring, training</description>
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5 <command interpreter="bash"><![CDATA[../../TaGRes-train
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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( $method ) != '' and str( $method ) != 'None' :
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22 -method "$method"
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23 #end if
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24 #if str( $function ) != '' and str( $function ) != 'None' :
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25 -function "$function"
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26 #end if
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27 #if str( $exp ) != '' and str( $exp ) != 'None' :
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28 -exp "$exp"
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29 #end if
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30 | tail -n 5
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31 ]]></command>
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32 <inputs>
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33 <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
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34 <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
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35 <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
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36 <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/>
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37 <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
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38 <option value="Rescoring3D">Rescoring3D</option>
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39 <option value="Rescoring4D">Rescoring4D</option>
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40 <option value="Rescoring1D">Rescoring1D</option>
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41 </param>
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42 <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
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43 <option value="MM">MM</option>
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44 <option value="PLP">PLP</option>
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45 </param>
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46 <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
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47 </inputs>
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48 <outputs>
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49 <data name="o" format="mod"/>
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50 </outputs>
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51 <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
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52 As input we need:
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53
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54 * a file containing a protonated protein in pdb-format
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55 * 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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56 * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein.
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57
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58 A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
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59
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60 The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help>
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61 </tool>