annotate macros.xml @ 3:e5fcba090b10 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a

<macros>
    <token name="@TOOL_VERSION@">3.0.20230403</token>
    <xml name="creator">
        <creator>
            <person
                givenName="Martin"
                familyName="Čech"
                url="https://github.com/martenson"
                identifier="0000-0002-9318-1781" />
            <person
                givenName="Karolína"
                familyName="Trachtová"
                url="https://github.com/trachtok" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI" />
        </creator>
    </xml>
    <token name="@HELP@">
        <![CDATA[
            BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota,
            as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification,
            based on the metabolism prediction.

            BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v3.

            Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and
            build upon the material under the condition that they must give appropriate credit, provide links to the license,
            and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be
            included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires
            explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer
            web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to
            acknowledge the authors.

            Parameters explanation:

            **Input.** Currently, only a CSV file with one SMILES per line is accepted.

            **The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut
            microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).

            **The number of steps for the prediction:** this option will be used for the EC-based, CYP450, Phase II, and Environmental
            microbial biotransformers. The default value is 1.

            **Mass tolerance for metabolite identification** (default is 0.01).

            **Output of BioTransformer** with CSV as an input are 3 TSV files. One without any filtering, second with filtered
            duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with
            filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP).

            (* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation
            first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable
            reaction(Oxidation, reduction, (de-)conjugation) at each step.
        ]]>
    </token>
</macros>