annotate macros.xml @ 0:7cda9aef13f3 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923

<macros>
    <token name="@TOOL_VERSION@">3.5.2</token>
    <xml name="requirements">
        <requirements>
            <container type="docker">recetox/recetox-msfinder:3.5.2-0</container>
        </requirements>
    </xml>
    <xml name="creator">
        <creator>
            <person
                givenName="Zargham"
                familyName="Ahmad"
                url="https://github.com/zargham-ahmad"
                identifier="0000-0002-6096-224X" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI" />
        </creator>
    </xml>
    <xml name="input">
        <param name="input_data" type="data" format="msp" label="Input mass spectral library file to which to add peak annotations."
            help="Formula and InChI (or SMILES) codes are required to be present in the library file" />
    </xml>
    <xml name="parameter">
        <param type="float" value="0.01" name="Ms2Tolerance" label="Ms2Tolerance" help="The mass tolerance used for fragment peak matching and annotation." />
        <param name="IsTmsMeoxDerivative" type="boolean" checked="False" truevalue="True" falsevalue="False" label="IsTmsMeoxDerivative"
            help="Check TMS-MeOX derivative to use EIMS database; otherwise, MSMS database is used." />
        <param type="integer" value="1" name="RelativeAbundanceCutOff" label="RelativeAbundanceCutOff"
            help="Remove peaks with less than specified % relative intensity from the spectra." />
        <param type="float" value="0.001" name="Ms1Tolerance" label="Ms1Tolerance" help="The precursor m/z tolerance to generate formula candidates." />
        <param type="select" name="MassToleranceType" label="MassToleranceType" help="Da stands for Daltons (amu), and Ppm stands for parts per million">
            <option value="Da" selected="True">Da</option>
            <option value="Ppm">Ppm</option>
        </param>
        <param type="integer" value="-1" name="StructurePredictionTimeOut" label="StructurePredictionTimeOut" help="Time out parameter, value of -1 means no timeout" />
        <param name="LewisAndSeniorCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="LewisAndSeniorCheck"
            help="Generate formula candidates that match the valence rules of formula elements." />
    </xml>
    <xml name="element_check_parameter">
        <!-- Element Checks -->
        <param name="Ocheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ocheck" />
        <param name="Ncheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ncheck" />
        <param name="Pcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Pcheck" />
        <param name="Scheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Scheck" />
        <param name="Fcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Fcheck" />
        <param name="ClCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="ClCheck" />
        <param name="BrCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="BrCheck" />
        <param name="Icheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Icheck" />
        <param name="SiCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="SiCheck" />
    </xml>
    <xml name="output">
        <data name="annotated_data" format="msp" />
    </xml>

    <token name="@HELP@"><![CDATA[
        **Description**

        MS-FINDER was launched as a universal program for compound annotation that supports EI-MS (GC/MS) and 
        MS/MS spectral mining. MS-FINDER provide solution for fragment annotations. The program can annotate 
        your unknowns by the public spectral databases such as MassBank, LipidBlast, and GNPS. MS-FINDER has 
        been developed as the collaborative work between Prof. Masanori Arita team (RIKEN, Reifycs Inc.) and 
        Prof. Oliver Fiehn team (UC Davis) supported by the JST/NSF SICORP Metabolomics for the low carbon society 
        project.

        This galaxy wrapper only peforms MS2 peak annotation given a correctly formatted mass spectral library file.
        FORMULA, PRECURSORMZ and SMILES (or INCHI) metadata entries are required to be present in the input mass spectral library file.
        Each spectrum has to be separated by a single blank line.

        For detailed documentation of the tool please visit https://mtbinfo-team.github.io/mtbinfo.github.io/MS-FINDER/tutorial
    ]]>
    </token>

    <xml name="citations">
        <citation type="doi">10.1021/acs.analchem.6b00770</citation>
    </xml>
</macros>