annotate CADDSuite-1.6/galaxyconfigs/tools/TaGRes.xml @ 8:dbb480e39d95 draft

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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="1.6">
    <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>