<!--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="simplerescorer" name="SimpleRescorer" version="1.6">
    <description>rescore docking results</description>
    <command interpreter="bash"><![CDATA[../../SimpleRescorer 
#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( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#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="function" optional="true" label="scoring function: 'MM', 'PLP' or 'PB'" type="select">
            <option value="MM">MM</option>
            <option value="PLP">PLP</option>
            <option value="PB">PB</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.
A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).

As input we need:
    * 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.

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>