Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite/galaxyconfigs/tools/TaGRes-train.xml @ 0:8ce0411aaeb3
Uploaded CADDSuite version 0.94
author | marcel |
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date | Sun, 26 Jun 2011 14:01:09 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Sun Jun 26 14:01:09 2011 -0400 @@ -0,0 +1,61 @@ + +<!--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.--> +<tool id="tagres-train" name="TaGRes-train" version="0.94"> + <description>Target-specific Grid-Rescoring, training</description> + <command interpreter="bash"><![CDATA[../../TaGRes-train +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $method ) != '' and str( $method ) != 'None' : + -method "$method" +#end if +#if str( $function ) != '' and str( $function ) != 'None' : + -function "$function" +#end if +#if str( $exp ) != '' and str( $exp ) != 'None' : + -exp "$exp" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> + <option value="Rescoring3D">Rescoring3D</option> + <option value="Rescoring4D">Rescoring4D</option> + <option value="Rescoring1D">Rescoring1D</option> + </param> + <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> + <option value="MM">MM</option> + <option value="PLP">PLP</option> + </param> + <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"/> + </inputs> + <outputs> + <data name="o" format="mod"/> + </outputs> + <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes). +As input we need: + + * a file containing a protonated protein in pdb-format + * 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). + * 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. + +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. + +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> +</tool> \ No newline at end of file