<!--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="ligcheck" name="LigCheck" version="1.1">
    <description>check molecules for errors</description>
    <command interpreter="bash"><![CDATA[../../LigCheck 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ef ) != ''  and str( $ef ) != 'None' :
   -ef "$ef"
#end if
#if str( $ri ) != ''  and str( $ri ) != 'None' :
   -ri
#end if
#if str( $ut ) != ''  and str( $ut ) != 'None' :
   -ut
#end if
#if str( $nc ) != ''  and str( $nc ) != 'None' :
   -nc
#end if
#if str( $rm ) != ''  and str( $rm ) != 'None' :
   -rm
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
        <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/>
        <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/>
        <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/>
        <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/>
        <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 checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).

The following checks are done for each molecule:

    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
    * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
    * each atom must have a valid assigned element
    * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
    * partial charges may not contain completely senseless values (&gt;5 or &lt;-5).
    * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.

If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help>
</tool>