<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Checks and evaluations]-->
<tool id="LigCheck" name="LigCheck" version="1.1.0">
  <description>check molecules for errors</description>
  <macros>
    <token name="@EXECUTABLE@">LigCheck</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>LigCheck

#if $param_i:
  -i $param_i
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_ef:
  -ef $param_ef
#end if
#if $param_ri:
  -ri $param_ri
#end if
#if $param_ut:
  -ut $param_ut
#end if
#if $param_nc:
  -nc $param_nc
#end if
#if $param_rm:
  -rm $param_rm
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file" help="(-i) "/>
    <param name="param_ef" type="float" value="0.5" label="error fraction; print error if fraction of invalid mols is large" help="(-ef) "/>
    <param name="param_ri" type="integer" min="0" max="1" optional="True" value="1" label="remove invalid molecules" help="(-ri) "/>
    <param name="param_ut" type="integer" min="0" max="1" optional="True" value="0" label="check for unique topologies" help="(-ut) "/>
    <param name="param_nc" type="integer" min="0" max="1" optional="True" value="0" label="no not check for unique conformations" help="(-nc) "/>
    <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" metadata_source="param_i" format="input"/>
  </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>