<tool id="matchms" name="matchMS" version="0.9.2+galaxy1">
    <description>calculate the similarity score and matched peaks</description>
    <requirements>
        <requirement type="package" version="0.9.2">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[
        sh ${matchms_python_cli}
    ]]> </command>

    <configfiles>
        <configfile name="matchms_python_cli">
            python3 ${__tool_directory__}/matchms_wrapper.py \
            $default_filters \
            $normalize_intensities \
            #if $symmetric.is_symmetric
                -s \
            #else
                --ref "$references" \
                --ref_format "$references.ext" \
            #end if
            "$queries" \
            "$queries.ext" \
            "$similarity_metric" \
            "$algorithm.tolerance" \
            "$algorithm.mz_power" \
            "$algorithm.intensity_power" \
            "$similarity_scores" \
            "$similarity_matches"
        </configfile>
    </configfiles>

    <inputs>
        <param label="Queries spectra" name="queries" type="data" format="msp,mgf" help="Query mass spectra to match against references." />
        <conditional name="symmetric">
            <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" />
        <when value="FALSE">
            <param label="Reference spectra" name="references" type="data" format="msp,mgf" help="Reference mass spectra to match against as library." />
        </when>
        </conditional>
        <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>
            <option value="ModifiedCosine">ModifiedCosine </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>
        <param name="default_filters" label="Default Filters" type="boolean" truevalue="-f" falsevalue="" checked="false"
            help="Apply default filters (make_charge_int, make_ionmode_lowercase, set_ionmode_na_when_missing, add_compound_name,
             derive_adduct_from_name, derive_formula_from_name, clean_compound_name, add_precursor_mz, derive_ionmode, correct_charge)."
        />
        <param name="normalize_intensities" label="Normalize Intensities" type="boolean" truevalue="-n" falsevalue="" checked="false" 
            help="Filter to normalize intensities."/>

    </inputs>

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

    <tests>
        <test>
            <param name="references" value="fill.mgf" ftype="mgf"/>
            <param name="queries" value="fill.msp" ftype="msp"/>
            <param name="similarity_metric" value="CosineGreedy"/>
            <output name="similarity_scores" file="scores_test1_out.tsv" ftype="tsv" checksum="md5$1aff8d0777e2f4e565be2b1b393547ef"/>
            <output name="similarity_matches" file="matches_test1_out.tsv" ftype="tsv" checksum="md5$aab26ef4a0e80a53699832db72c06340"/>
        </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="scores_test2_out.tsv" ftype="tsv" checksum="md5$d2a5a01d9980636ce6a246d68834b84e"/>
            <output name="similarity_matches" file="matches_test2_out.tsv" ftype="tsv" checksum="md5$28dc16ce45105234437e53d59e240046"/>
        </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"/>
            <param name="default_filters" value="TRUE" />
            <output name="similarity_scores" file="scores_test3_out.tsv" ftype="tsv" checksum="md5$1341369778036e0a267ff723f8cfca9c"/>
            <output name="similarity_matches" file="matches_test3_out.tsv" ftype="tsv" checksum="md5$28dc16ce45105234437e53d59e240046"/>
        </test>
        <test>
            <param name="references" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="queries" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="similarity_metric" value="ModifiedCosine"/>
            <output name="similarity_scores" file="scores_test4_out.tsv" ftype="tsv"/>
            <output name="similarity_matches" file="matches_test4_out.tsv" ftype="tsv"/>
        </test>
        <test>
            <param name="queries" value="fill.msp" ftype="msp"/>
            <param name="similarity_metric" value="CosineHungarian"/>
            <param name="is_symmetric" value="TRUE"/>
            <output name="similarity_scores" file="scores_test5_out.tsv" ftype="tsv"/>
            <output name="similarity_matches" file="matches_test5_out.tsv" ftype="tsv"/>
        </test>
        <test>
            <param name="references" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="queries" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="similarity_metric" value="ModifiedCosine"/>
            <param name="normalize_intensities" value="TRUE"/>
            <output name="similarity_scores" file="scores_test6_out.tsv" ftype="tsv"/>
            <output name="similarity_matches" file="matches_test6_out.tsv" ftype="tsv"/>
        </test>
            <test>
            <param name="references" value="recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
            <param name="queries" value="fill.msp" ftype="msp"/>
            <param name="normalize_intensities" value="TRUE"/>
            <param name="similarity_metric" value="CosineHungarian"/>
            <output name="similarity_scores" file="scores_test7_out.tsv" ftype="tsv"/>
            <output name="similarity_matches" file="matches_test7_out.tsv" ftype="tsv"/>
        </test>
    </tests>

    <help><![CDATA[
    Documentation
        For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst and 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 outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks.
    ]]></help>


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