<?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: [Convert, combine and store]-->
<tool id="MolCombine" name="MolCombine" version="1.1.0">
  <description>combine molecular files</description>
  <macros>
    <token name="@EXECUTABLE@">MolCombine</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MolCombine

#if $param_i1:
  -i1 $param_i1
#end if
#if $param_i2:
  -i2 $param_i2
#end if
#if $param_mode:
  -mode
  #if " " in str($param_mode):
    "$param_mode"
  #else
    $param_mode
  #end if
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_ignH:
  -ignH $param_ignH
#end if
#if $param_replace_prop:
  -replace_prop $param_replace_prop
#end if
#if $param_rm:
  -rm $param_rm
#end if
</command>
  <inputs>
    <param name="param_i1" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file A" help="(-i1) "/>
    <param name="param_i2" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file B" help="(-i2) "/>
    <param name="param_mode" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'intersection', 'union' or 'b_not_a'" help="(-mode) ">
      <option value="intersection">intersection</option>
      <option value=" union"> union</option>
      <option value=" b_not_a"> b_not_a</option>
    </param>
    <param name="param_ignH" type="integer" min="0" max="1" optional="True" value="1" label="ignore hydrogens, i.e" help="(-ignH) match molecules to any protonation state"/>
    <param name="param_replace_prop" type="integer" min="0" max="1" optional="True" value="0" label="replace properties from file 1 w/ those from file 2" help="(-replace_prop) "/>
    <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files when finished" help="(-rm) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" metadata_source="param_i1" format="input"/>
  </outputs>
  <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.

If you want to match molecules regardless of their protonation state, use option '-ignH'.

Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.

</help>
</tool>