annotate macros.xml @ 1:c1a9c990d4b0 draft

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

<macros>
    <token name="@TOOL_VERSION@">3.0.0</token>

    <xml name="creator">
        <creator>
            <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[
        RMassBank workflow - part I and II
            This is implementation of RMassBank workflow (Bioconductor R package) based on publication by Stravs et al. 2013.

            Original RMassBank package is used to process tandem MS files and build MassBank records. Functions include
            automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem
            MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet
            databases, and export to MassBank records.

            This script is a full pipeline of RmassBank that loads settings file, compounds list, infolist and input .mzML
            files (one or multiple) and goes through all 8 steps of data-preprocessing referenced in RMassBank's
            Bioconductor manual (Mass spectrometry workflow, function msmsWorkflow()) and all steps of MassBank record
            generation (MassBank record workflow, function mbWorkflow()). To make it easier for user, based on template
            of settings required by RMassBank package the corresponding settings file is created as well
            (see section Settings file).

            User's inputs:
                - *compounds list* **(must have suffix .csv)** - separator must be ',', required columns: ID, Name_deu, Name_Eng, Name, SMILES, RT, CAS
                - *mode* - either **pH** (positive H) specifies [M+H]+ OR **pNa** specifies [M+Na]+ OR **pM** specifies [M]+ OR **mFA** specify [M-H]- and [M+FA]-
                - *input mzML files* - files for RMassBank package must have specific naming, each filename should be in format: xxxxxxxx_1234_xxx.mzXML where the xxx denotes anything and 1234 is compound ID (must be stated in ID column of compound csv file).
                - *infolist* **(must have suffix .csv)** - separator must be ',', columns (required columns are **bold**): '' (column name empty, values are numbers from 1 to n=number of chemicals), OK, id, dbcas, dbname_d, dbname_e, dataused, COMMENT.CONFIDENCE, COMMENT.EAWAG_UCHEM_ID, **CH$NAME1**, CH$NAME2, CH$NAME3, CH$COMPOUND_CLASS, **CH$FORMULA**, **CH$EXACT_MASS**, **CH$SMILES**, **CH$IUPAC**, CH$LINK.CAS, CH$LINK.CHEBI, CH$LINK.HMDB, CH$LINK.KEGG, CH$LINK.LIPIDMAPS, CH$LINK.PUBCHEM, **CH$LINK.INCHIKEY**, CH$LINK.CHEMSPIDER
                - *settings parameters* - either filled in Galaxy or the whole settings file can be uploaded and used to run the RMassBank workflow

            Galaxy outputs:
                - CSV file with failed peaks (empty if there were no failed peaks)
                - PDF plot showing performance of the recalibration
                - Full R environment (.RData) that should be used as an input for RMassBank workflow - part II
                - R environment with re-analyzed spectra (_RA.RData, see RMassBank manual for more information)
                - R environment with refiltered spectra (_RF.RData, see RMassBank manual for more information)
                - *zipped folder* with records ready to be uploaded to MassBank database
                - *settings file* used to run the RMassBank

                For more information about the data-preprocessing and record generation of the RMassBank pipeline, please refer
                to `Bioconductor manual <https://www.bioconductor.org/packages/release/bioc/html/RMassBank.html>`_ for RMassBank.

            Settings file
                In the original RMassBank R package, user has to specify multiple parameters via the settings file. To make
                life easier for users of this tool, most of the parameters can be specified in the Galaxy intrface for this
                tool and are automatically filled in the settings template that can is then used for RMassBank workflow.
                If the user wants to supply his/her own settings files, that is also possible. Path to OpenBabel will be
                automatically filled no matter what is the original specification in the supplied settings file.

                For all parameters, please refer to the manual for RMassBank at `Bioconductor website
                <https://www.bioconductor.org/packages/release/bioc/html/RMassBank.html>`_ .

            Parameters that can only be changed manually are:
                - *deprofile:* leave empty if input data are already in centroid mode (usuall case), otherwise use one of the values from deprofile.spline, deprofile.fwhm or deprofile.localMax to convert the input $
                - *babeldir:* do not change this if the settings file is to be further used in Galaxy
                - *annotations:* several fields containg information about author, used instrument etc.
                - *spectraList:* list of data-dependent scans in their order (relative to the parent scan), for annotation of the MassBank records
                - *electronicNoise:* list of known electronic noise peaks
                - *recalibrator:* custom recalibration function
                - *titleFormat:* defines the title format

                **All parameters are more thoroughly described in the created settings file, which can be edited in any simple
                text editor.**

                **NOTE:** In case of manual editing of the settings file, do not indent with TAB characters! Use only spaces.

        Authors of RMassBank: Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions
        from Tobias Schulze.

        RMassBank maintainer: at Eawag ([e-mail])
        ]]>
    </token>
</macros>