annotate macros.xml @ 5:a177ac3c752c draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e

<macros>
    <token name="@TOOL_VERSION@">0.20.0</token>

    <xml name="creator">
        <creator>
            <yield/>
            <person
                givenName="Helge"
                familyName="Hecht"
                url="https://github.com/hechth"
                identifier="0000-0001-6744-996X" />
            <person
                givenName="Maksym"
                familyName="Skoryk"
                url="https://github.com/maximskorik"
                identifier="0000-0003-2056-8018" />
            <person
                givenName="Zargham"
                familyName="Ahmad"
                url="https://github.com/zargham-ahmad"
                identifier="0000-0002-6096-224X" />
            <person
                givenName="Wudmir"
                familyName="Rojas"
                url="https://github.com/wverastegui"
                identifier="0000-0001-7036-9987" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI" />
        </creator>
    </xml>
    
    <xml name="bio.tools">
        <xrefs>
            <xref type="bio.tools">matchms</xref>
        </xrefs>
    </xml>

    <xml name="similarity_metrics">
        <option value="CosineGreedy" selected="true">CosineGreedy</option>
        <option value="CosineHungarian">CosineHungarian</option>
        <option value="ModifiedCosine">ModifiedCosine</option>
        <option value="NeutralLossesCosine">NeutralLossesCosine</option>
    </xml>

    <xml name="similarity_algorithm_params">
        <section name="algorithm" title="Algorithm Parameters" expanded="true">
            <param label="tolerance [Da]" 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>
    </xml>

    <xml name="input_param">
        <conditional name="scores">
            <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
                   checked="false"/>
            <when value="TRUE">
                <param label="Scores object" name="scores_in" type="data" format="json"
                    help="Scores objects calculated previously using one of the matchms similarity tools." />
                <param label="join type" name="join_type" type="select" display="radio"
                    help="The join type to use for appending scores - see [1] for details.">
                    <option value="left" selected="true">left</option>
                    <option value="inner">inner</option>
                    <option value="right">right</option>
                    <option value="outer">outer</option>
                </param>
            </when>
            <when value="FALSE">
                <param label="Queries spectra" name="queries" type="data" format="msp"
                    help="Query mass spectra to match against references."/>
                <param label="Reference spectra" name="references" type="data" format="msp"
                    help="Reference mass spectra to match against as library."/>
            </when>
        </conditional>
    </xml>

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

<token name="@init_scores@">
from matchms.importing import load_from_msp, scores_from_json
from matchms import Scores
#if $scores.use_scores
scores = scores_from_json("$scores_in")
join_type = "$scores.join_type"
#else
scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
join_type = "left"
#end if
</token>

<token name="@init_logger@">
from matchms import set_matchms_logger_level
set_matchms_logger_level("WARNING")
</token>   
</macros>