<tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy0">
    <description>filter and normalize mass spectrometry data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
        <requirement type="package" version="1.1.4">pandas</requirement>
    </requirements>

    <environment_variables>
        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
    </environment_variables>

    <command detect_errors="exit_code"><![CDATA[
        sh ${matchms_python_cli}
    ]]> </command>

    <configfiles>
        <configfile name="matchms_python_cli">
            python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
            --spectra "$spectra" \
            --spectra_format "$spectra.ext" \
            #if $normalise_intensities.is_true
                -normalise_intensities \
            #end if
            #if $default_filters.is_true
                -default_filters \
            #end if
            #if $clean_metadata.is_true
                -clean_metadata \
            #end if
            #if $relative_intensity.is_true
                -relative_intensity \
                --from_intensity "$relative_intensity.from_intensity" \
                --to_intensity "$relative_intensity.to_intensity" \
            #end if
            #if $mz_range.is_true
                -mz_range \
                --from_mz "$mz_range.from_mz" \
                --to_mz "$mz_range.to_mz" \
            #end if
            --output "$output"
        </configfile>
    </configfiles>

    <inputs>
        <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />

        <conditional name="normalise_intensities">
            <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Normalize intensities of peaks (and losses) to unit height."/>
        </conditional>

        <conditional name="default_filters">
            <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
        </conditional>

        <conditional name="clean_metadata">
            <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
        </conditional>

        <conditional name="relative_intensity">
            <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
            <when value="TRUE">
                <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." />
                <param label="Maximum intensity" name="to_intensity" optional="true" type="float" help="Upper bound for intensity filter." />
            </when>
        </conditional>

        <conditional name="mz_range">
            <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." />
            <when value="TRUE">
                <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
                <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
            </when>
        </conditional>

    </inputs>

    <outputs>
        <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
    </outputs>

    <tests>
        <test>
            <param name="spectra" value="filtering/input.msp" ftype="msp"/>
            <section name="normalise_intensities">
                <param name="is_true" value="TRUE"/>
            </section>
            <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectra" value="filtering/input.msp" ftype="msp"/>
            <section name="default_filters">
                <param name="is_true" value="TRUE"/>
            </section>
            <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectra" value="filtering/input.msp" ftype="msp"/>
            <section name="clean_metadata">
                <param name="is_true" value="TRUE"/>
            </section>
            <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectra" value="filtering/input.msp" ftype="msp"/>
            <section name="relative_intensity">
                <param name="is_true" value="TRUE"/>
                <param name="from_intensity" value="0.3"/>
                <param name="to_intensity" value="0.9"/>
            </section>
            <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectra" value="filtering/input.msp" ftype="msp"/>
            <section name="mz_range">
                <param name="is_true" value="TRUE"/>
                <param name="from_mz" value="300"/>
                <param name="to_mz" value="800"/>
            </section>
            <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
        </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 output is an msp file after applying the specified filters.
    ]]></help>


    <citations>
        <citation type="doi">10.5281/zenodo.7178586</citation>
        <citation type="doi">10.21105/joss.02411</citation>
    </citations>
</tool>