<tool id="ctb_openmg" name="Open Molecule Generator" version="0.2">
    <description>- exhaustive generation of chemical structures</description>
    <requirements>
        <requirement type="package" version="0.1">openmg</requirement>
        <requirement type="package">java-jdk</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
        openmg
            -ec '$ec'
            #if $fr:
                -fr '$sdf_outfile'
            #end if
            -o '$outfile'
]]>
    </command>
    <inputs>
        <param argument="-ec" type="text" label="Elemental composition of the molecules to be generated"
            help="e.g. C2H5NO2"/>
        <param name='fr' type='boolean' truevalue='-fr' falsevalue='' label='Output SD-file containing prescribed (single or multiple) substructure(s)'
            help="In the case of multiple substructures, they must be non-overlapping" />
    </inputs>
    <outputs>
        <data format="sdf" name="outfile" />
        <data format="sdf" name="sdf_outfile">
            <filter>fr is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="ec" value="C6H6"/>
            <output name="outfile" file="openmg_results.sdf" lines_diff="440"/>
        </test>
    </tests>
    <help>
<![CDATA[
.. class:: infomark

**What this tool does**

Takes an molecular formula (such as C6H6, C2H5NO2) and returns all possible structures with this elemental composition.

]]>
    </help>
    <citations>
        <citation type="doi">10.1186/1758-2946-4-21</citation>
    </citations>
</tool>