annotate matchms_formatter.xml @ 0:60f34912b3de draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"

<tool id="matchms_formatter" name="matchms output formatter" version="0.1.3" 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,tabular,tsv" help="Scores output table." />
        <param label="Matches Table" name="matches" type="data" format="csv,tabular,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[
    Usage
        This tool creates user friendly tables from the data matrices produces by matchms.
        The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.

    Input Table Format
        The tool expects two data matrices with the format as depicted below.
        The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).

        +----------+------+------+-----+
        |          | C001 | C002 | ... |
        +==========+======+======+=====+
        | Perylene | 0.1  | 0.0  | ... |
        +----------+------+------+-----+
        | Glycine  | 0.5  | 0.34 | ... |
        +----------+------+------+-----+
        |   ...    | ...  | ...  | ... |
        +----------+------+------+-----+

    Output Table Format
        +----------+-----------+---------+--------+
        | query    | reference | matches | scores |
        +==========+===========+=========+========+
        | C001     | Glycine   |      6  | 0.5    |
        +----------+-----------+---------+--------+
        | C002     | Glycine   |     3   | 0.34   |
        +----------+-----------+---------+--------+
        |   ...    | ...       | ...     | ...    |
        +----------+-----------+---------+--------+

    ]]></help>
</tool>