Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite/galaxyconfigs/tools/TaGRes.xml @ 3:bb26168c5715
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author | marcel |
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date | Tue, 12 Jul 2011 10:53:07 -0400 |
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children | af446ca2d5c6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml Tue Jul 12 10:53:07 2011 -0400 @@ -0,0 +1,67 @@ + +<!--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="0.95"> + <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 + | 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="data"/> + <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> + </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> \ No newline at end of file