<tool id="matchms" name="matchMS" version="0.8.2+galaxy3">
    <requirements>
        <requirement type="package" version="0.8.2">matchms</requirement>
        <requirement type="package" version="1.1.4">pandas</requirement>
    </requirements>

    <environment_variables>
        <environment_variable name="MPLCONFIGDIR">/tmp</environment_variable>
    </environment_variables>

    <command detect_errors="exit_code"><![CDATA[
        python3 ${__tool_directory__}/matchms_wrapper.py "$references" "$queries" "$similarity_metric" "$similarity_scores" "$similarity_matches" "$algorithm.tolerance" "$algorithm.mz_power" "$algorithm.intensity_power"
    ]]> </command>

    <inputs>
        <param label="Reference spectra" name="references" type="data" format="msp" help="Reference mass spectra to match against as library." />
        <param label="Queries spectra" name="queries" type="data" format="msp" help="Query mass spectra to match against references." />
        <param label="Similarity metric" name="similarity_metric" type="select" display="radio" help="Similarity metric to use for score computation.">
            <option value="CosineGreedy" selected="true">CosineGreedy</option>
            <option value="CosineHungarian">CosineHungarian</option>
        </param>

        <section name="algorithm" title="Algorithm Parameters" expanded="true">    
            <param label="tolerance" name="tolerance" type="float" value="0.1" help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm." />
            <param label="mz_power" name="mz_power" type="float" value="0.0" help="The power to raise mz to in the cosine function." />
            <param label="intensity_power" name="intensity_power" type="float" value="1.0" help="The power to raise intensity to in the cosine function." />
        </section>
    </inputs>

    <outputs>
        <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="csv" />
        <data label="$similarity_metric matches of ${on_string}" name="similarity_matches" format="csv" />
    </outputs>

    <tests>
        <test>
            <param name="references" value="fill.msp" ftype="msp"/>
            <param name="queries" value="fill.msp" ftype="msp"/>
            <param name="similarity_metric" value="CosineGreedy"/>
            <output name="similarity_scores" file="symmetric_fill_cosine_greedy.csv" ftype="csv" checksum="md5$1be210e4a219f6a9315d6ca840d89247"/>
            <output name="similarity_matches" file="matches_symmetric_fill_greedy.csv" ftype="csv" checksum="md5$93a43a55e02c099581e5765d6ead9f13"/>
        </test>
        <test>
            <param name="references" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="queries" value="fill.msp" ftype="msp"/>
            <param name="similarity_metric" value="CosineGreedy"/>
            <output name="similarity_scores" file="rcx_fill_cosine_greedy.csv" ftype="csv" checksum="md5$f9f9e3f9483de9486658fcdbba92451e"/>
            <output name="similarity_matches" file="matches_rcx_fill_greedy.csv" ftype="csv" checksum="md5$4aadb19c261fa41907d80f2d326055b6"/>
        </test>
        <test>
            <param name="references" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="queries" value="fill.msp" ftype="msp"/>
            <param name="similarity_metric" value="CosineHungarian"/>
            <output name="similarity_scores" file="rcx_fill_cosine_hungarian.csv" ftype="csv" checksum="md5$e4063294e0f70e0e966a252ec43a1537"/>
            <output name="similarity_matches" file="matches_rcx_fill_hungarian.csv" ftype="csv" checksum="md5$4aadb19c261fa41907d80f2d326055b6"/>
        </test>
    </tests>

    <help><![CDATA[
    Documentation
        For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst or for more details https://matchms.readthedocs.io/en/latest/.

    Upstream Tools
        +-----------+---------------+--------+-----------+
        | Name      | Output File   | Format | Parameter |
        +===========+===============+========+===========+
        | RAMClustR | Mass spectra  | msp    | references|
        +-----------+---------------+--------+-----------+
        | RAMClustR | Mass spectra  | msp    | queries   |
        +-----------+---------------+--------+-----------+

    Downstream Tools
        The **output** is a csv which contains the similarity score and second csv containing the number of matched peaks.
    ]]></help>


    <citations>
        <citation type="doi">10.5281/zenodo.4589154</citation>
        <citation type="doi">10.21105/joss.02411</citation>
    </citations>
</tool>