<!--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="molcombine" name="MolCombine" version="0.9.6">
    <description>combine molecular files</description>
    <command interpreter="bash"><![CDATA[../../MolCombine 
#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
   -i1 "$i1"
#end if
#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
   -i2 "$i2"
#end if
#if str( $mode ) != ''  and str( $mode ) != 'None' :
   -mode "$mode"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ignH ) != ''  and str( $ignH ) != 'None' :
   -ignH
#end if
#if str( $replace_prop ) != ''  and str( $replace_prop ) != 'None' :
   -replace_prop
#end if
#if str( $rm ) != ''  and str( $rm ) != 'None' :
   -rm
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/>
        <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/>
        <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select">
            <option value="intersection">intersection</option>
            <option value="union">union</option>
            <option value="b_not_a">b_not_a</option>
        </param>
        <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/>
        <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/>
        <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="o" format="mol2/sdf/drf" format_source="i1"/>
    </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>