<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09">
    <description>Semiempirical quantum mechanical molecular optimization method</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">xtb</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '${coordinates}' 'mol.${coordinates.ext}' &&
        xtb 'mol.${coordinates.ext}' --opt '${opt_level}' && 
        cp 'xtbopt.${coordinates.ext}' '${output}'
    ]]></command>
    <inputs>
        <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/>
        <param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." >
            <option value="crude">crude</option>
            <option value="sloppy">sloppy</option>
            <option value="loose">loose</option>
            <option value="lax">lax</option>
            <option value="normal">normal</option>
            <option value="tight">tight</option>
            <option value="vtight">vtight</option>
            <option value="extreme">extreme</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="coordinates"  />
    </outputs>
    <tests>
        <test>
            <param name="coordinates" value="initial_mol.xyz" ftype="xyz"/>
            <output name="output">
                <assert_contents>
                    <has_text text="xtb"/>
                    <has_n_lines n="26"/> 
                </assert_contents>
            </output>
        </test>
        <!-- <test>
            <param name="coordinates" value="initial_mol.coord" ftype="coord"/>
            <output name="output" file="optimized_mol.coord" ftype="coord">
                <assert_contents>
                    <has_text text="$coord"/>
                    <has_n_lines min="26"/> 
                </assert_contents>
            </output>
        </test> -->
    </tests> 
    <help>
        <![CDATA[
        @HELP@
        ]]>
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1002/wcms.1493</citation>
    </citations>
</tool>