Mercurial > repos > marcel > caddsuite_mac10_6
view CADDSuite-1.1/galaxyconfigs/tools/TaGRes.xml @ 6:decca54699e3
Uploaded Version 1.1
author | marcel |
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date | Thu, 12 Jan 2012 11:07:03 -0500 |
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<!--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" name="TaGRes" version="1.1"> <description>Target-specific Grid-Rescoring</description> <command interpreter="bash"><![CDATA[../../TaGRes #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( $mod ) != '' and str( $mod ) != 'None' : -mod "$mod" #end if #if str( $tf ) != '' and str( $tf ) != 'None' : -tf "$tf" #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( $rm ) != '' and str( $rm ) != 'None' : -rm #end if | tail -n 5 ]]></command> <inputs> <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="mod"/> <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=""/> <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select"> <option value="Rescoring3D">Rescoring3D</option> <option value="Rescoring4D">Rescoring4D</option> <option value="Rescoring1D">Rescoring1D</option> </param> <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select"> <option value="MM">MM</option> <option value="PLP">PLP</option> </param> <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/> </outputs> <help>This tool rescores docking output poses using Target-specific Grid-Rescoring. Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool. As input TaGRes needs: * 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 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. * a regression model file as generated by TaGRes-train for same protein target than the one specified here. 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. 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> </tool>