comparison CADDSuite/galaxyconfigs/tools/TaGRes-train.xml @ 5:b7a89b15646f

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4:02c8570cde57

<!--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

   -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).

    * 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>

5:b7a89b15646f

<!--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="0.95">
    <description>Target-specific Grid-Rescoring, training</description>
    <command interpreter="bash"><![CDATA[../../TaGRes-train 
#if str( $rec ) != ''  and str( $rec ) != 'None' :
   -rec "$rec"
#end if

   -exp "$exp"
#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="training compound data set" type="data" format="mol2/sdf/drf"/>
        <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="exp" optional="false" label="property-tag name containing experimentally determined binding-free-energies" 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).

    * 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 is 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 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>