<tool id="matchms_formatter" name="matchms output formatter" version="0.1.1" python_template_version="3.5">
    <description>reformat output tables of matchms</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <requirements>
        <requirement type="package" version="1.1.4">pandas</requirement>
        <requirement type="package" version="8.0.1">click</requirement>
    </requirements>

    <command detect_errors="aggressive"><![CDATA[
        sh ${matchms_formatter_cli}
    ]]></command>

    <configfiles>
        <configfile name="matchms_formatter_cli">
            python3 ${__tool_directory__}/formatter.py \
            --sf "$scores" \
            --mf "$matches" \
            --o "$output" \
            $method.selection \
            #if $method.selection == "get-thresholded-data"
            --st $method.scores_threshold \
            --mt $method.matches_threshold
            #else
            --k $method.k
            #end if
        </configfile>
    </configfiles>

    <inputs>
        <param label="Scores Table" name="scores" type="data" format="csv,tsv" help="Scores output table."/>
        <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table."/>

        <conditional name="method">
            <param name="selection" type="select" label="Formatting method">
                <option value="get-thresholded-data" selected="true">Thresholding</option>
                <option value="get-top-k-data">Top K Matches</option>
            </param>
            <when value="get-thresholded-data">
                <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
                       help="Threshold for matching score."/>
                <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
                       help="Threshold for number of matches ions."/>
            </when>
            <when value="get-top-k-data">
                <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
            </when>
        </conditional>

    </inputs>
    <outputs>
        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores"/>
    </outputs>

    <tests>
        <test>
            <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
            <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
            <param name="selection" value="get-thresholded-data"/>
            <param name="scores_threshold" value="0.4"/>
            <param name="matches_threshold" value="2"/>
            <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv" 
                    checksum="md5$8929cdac47252da638f066261ffc16b7"/>
        </test>
        <test>
            <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
            <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
            <param name="selection" value="get-top-k-data"/>
            <param name="k" value="3"/>
            <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
                    checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
        </test>
    </tests>

    <help>
        <![CDATA[
            @HELP_formatter@
        ]]>
    </help>
</tool>