<!--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="pocketdetector" name="PocketDetector" version="1.6">
    <description>detect binding pocket</description>
    <command interpreter="bash"><![CDATA[../../PocketDetector 
#if str( $rec ) != ''  and str( $rec ) != 'None' :
   -rec "$rec"
#end if
#if str( $rl ) != ''  and str( $rl ) != 'None' :
   -rl "$rl"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ini ) != ''  and str( $ini ) != 'None' :
   -ini "$ini"
#end if
#if str( $p ) != ''  and str( $p ) != 'None' :
   -p "$p"
#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="input ini file" type="data" format="ini"/>
        <param name="p" optional="true" label="Optional: penalty value" type="text" area="true" size="1x5" value="5e11"/>
    </inputs>
    <outputs>
        <data name="o" format="ini"/>
    </outputs>
    <help>This tool tries to detect the binding pocket in which the reference ligand is located.
Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket.

As input we need:
    * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder.
    * 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).

Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring.</help>
</tool>