annotate CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml @ 5:b7a89b15646f

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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="antitargetrescorer" name="AntitargetRescorer" version="0.95">
    <description>rescore w/ anti-target dock-results</description>
    <command interpreter="bash"><![CDATA[../../AntitargetRescorer 
#if str( $t ) != ''  and str( $t ) != 'None' :
   -t "$t"
#end if
#if str( $at ) != ''  and str( $at ) != 'None' :
   -at "$at"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="t" optional="false" label="input file w/ target dock-results" type="data" format="mol2/sdf/drf"/>
        <param name="at" optional="false" label="input file w/ anti-target dock-results" type="data" format="mol2/sdf/drf"/>
    </inputs>
    <outputs>
        <data name="o" format="mol2/sdf/drf" format_source="t"/>
    </outputs>
    <help>This tool rescores docking output poses.
AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.

As input we need:
    * 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 docket into the specified protein (i.e. the target).
    * a file containing the same compounds docked into the antitarget.

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 'antitarget_rescore'.</help>
</tool>