<?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: [Preparation]-->
<tool id="SeperateMolecules" name="SeperateMolecules" version="1.1.0">
  <description>Split each multi molecule entry to separate single molecule entries</description>
  <macros>
    <token name="@EXECUTABLE@">SeperateMolecules</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SeperateMolecules

#if $param_i:
  -i $param_i
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_min_atoms:
  -min_atoms $param_min_atoms
#end if
#if $param_all:
  -all $param_all
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="sdf,sd,mol2,mol" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file (mol mol2 sd sdf)" help="(-i) "/>
    <param name="param_min_atoms" type="integer" value="0" label="only keep molecules having at least a minimal number of atoms" help="(-min_atoms) "/>
    <param name="param_all" type="integer" min="0" max="1" optional="True" value="0" label="keep all contained molecules, but each in separated entries" help="(-all) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" metadata_source="param_i" format="input"/>
  </outputs>
  <help>This tool splits each molecule entry contained in a structure file (mol, sdf, mol2) into possibly multiple molecule entries, so that the new entries contain only a single connected molecule. The results will always be written to a single structure file in the same format as the input format, or a sdf-file in the case of a mol input file. The tool works with the given bond information, which needs to be correct.

Standard behaviour: only the largest molecule from each entry is retained ('largest' according to the number of atoms).

Optional parameters:
Retain all molecules contained in a molecule entry ('-all'). Alternatively the minimal number of atoms required for a molecule to be kept can be specified ('-min_atoms').

</help>
</tool>