annotate macros.xml @ 12:a6af1e124e06 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d

<macros>
    <token name="@TOOL_VERSION@">0.3.0</token>

    <xml name="creator">
        <creator>
            <person
                givenName="Matej"
                familyName="Troják"
                url="https://github.com/xtrojak"
                identifier="0000-0003-0841-2707" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI" />
        </creator>
    </xml>

    <token name="@HELP@">
        <![CDATA[
        MSMetaEnhancer will fetch and update various metadata included in your spectra dataset.
        It does so through a series of conversions ran on all entries in a given file. These conversions fetch
        metadata from various online services. If no conversions are specified, all possible jobs will be executed in an arbitrary order.

        Every conversion specifies `service`, `source` and `target` attributes. This can be read as the `service` will receive the `source` attribute
        and based on that determines the `target` attribute. For example, the conversion `PubChem: inchi -> smiles` uses PubChem to convert
        InChI to SMILES.

        The execution speed and results themselves can be affected by specifying the conversions, or their order.

        For detailed documentation of the tool please visit https://msmetaenhancer.readthedocs.io/.

        ## Developer instructions

        When updating this tool, it is necessary to make sure that `job_options` in `macros.xml` config file are up-to-date.
        This can be done by running `galaxy/generate_options.py` script in [MSMetaEnhancer](https://github.com/RECETOX/MSMetaEnhancer) tool and 
        copying generated options to the macro.

    ]]>
    </token>

    <xml name="job_options">
        <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option>
        <option value="inchi canonical_smiles RDKit">RDKit: inchi -> canonical_smiles</option>
        <option value="inchi isomeric_smiles RDKit">RDKit: inchi -> isomeric_smiles</option>
        <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option>
        <option value="smiles mw RDKit">RDKit: smiles -> mw</option>
        <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option>
        <option value="compound_name formula IDSM">IDSM: compound_name -> formula</option>
        <option value="compound_name inchi IDSM">IDSM: compound_name -> inchi</option>
        <option value="compound_name inchikey IDSM">IDSM: compound_name -> inchikey</option>
        <option value="compound_name isomeric_smiles IDSM">IDSM: compound_name -> isomeric_smiles</option>
        <option value="compound_name iupac_name IDSM">IDSM: compound_name -> iupac_name</option>
        <option value="inchi canonical_smiles IDSM">IDSM: inchi -> canonical_smiles</option>
        <option value="inchi formula IDSM">IDSM: inchi -> formula</option>
        <option value="inchi inchikey IDSM">IDSM: inchi -> inchikey</option>
        <option value="inchi isomeric_smiles IDSM">IDSM: inchi -> isomeric_smiles</option>
        <option value="inchi iupac_name IDSM">IDSM: inchi -> iupac_name</option>
        <option value="iupac_name inchi IDSM">IDSM: iupac_name -> inchi</option>
        <option value="casno inchi CTS">CTS: casno -> inchi</option>
        <option value="casno inchikey CTS">CTS: casno -> inchikey</option>
        <option value="compound_name inchikey CTS">CTS: compound_name -> inchikey</option>
        <option value="hmdbid inchi CTS">CTS: hmdbid -> inchi</option>
        <option value="inchikey compound_name CTS">CTS: inchikey -> compound_name</option>
        <option value="inchikey inchi CTS">CTS: inchikey -> inchi</option>
        <option value="inchikey iupac_name CTS">CTS: inchikey -> iupac_name</option>
        <option value="casno smiles CIR">CIR: casno -> smiles</option>
        <option value="inchi smiles CIR">CIR: inchi -> smiles</option>
        <option value="inchikey casno CIR">CIR: inchikey -> casno</option>
        <option value="inchikey formula CIR">CIR: inchikey -> formula</option>
        <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option>
        <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option>
        <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option>
        <option value="compound_name canonical_smiles PubChem">PubChem: compound_name -> canonical_smiles</option>
        <option value="compound_name formula PubChem">PubChem: compound_name -> formula</option>
        <option value="compound_name inchi PubChem">PubChem: compound_name -> inchi</option>
        <option value="compound_name inchikey PubChem">PubChem: compound_name -> inchikey</option>
        <option value="compound_name isomeric_smiles PubChem">PubChem: compound_name -> isomeric_smiles</option>
        <option value="compound_name iupac_name PubChem">PubChem: compound_name -> iupac_name</option>
        <option value="inchi canonical_smiles PubChem">PubChem: inchi -> canonical_smiles</option>
        <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
        <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
        <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option>
        <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
        <option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option>
        <option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option>
        <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option>
        <option value="chebiid chemspiderid BridgeDb">BridgeDb: chebiid -> chemspiderid</option>
        <option value="chebiid hmdbid BridgeDb">BridgeDb: chebiid -> hmdbid</option>
        <option value="chebiid keggid BridgeDb">BridgeDb: chebiid -> keggid</option>
        <option value="chebiid pubchemid BridgeDb">BridgeDb: chebiid -> pubchemid</option>
        <option value="chebiid wikidataid BridgeDb">BridgeDb: chebiid -> wikidataid</option>
        <option value="chemspiderid chebiid BridgeDb">BridgeDb: chemspiderid -> chebiid</option>
        <option value="chemspiderid hmdbid BridgeDb">BridgeDb: chemspiderid -> hmdbid</option>
        <option value="chemspiderid keggid BridgeDb">BridgeDb: chemspiderid -> keggid</option>
        <option value="chemspiderid pubchemid BridgeDb">BridgeDb: chemspiderid -> pubchemid</option>
        <option value="chemspiderid wikidataid BridgeDb">BridgeDb: chemspiderid -> wikidataid</option>
        <option value="hmdbid chebiid BridgeDb">BridgeDb: hmdbid -> chebiid</option>
        <option value="hmdbid chemspiderid BridgeDb">BridgeDb: hmdbid -> chemspiderid</option>
        <option value="hmdbid keggid BridgeDb">BridgeDb: hmdbid -> keggid</option>
        <option value="hmdbid pubchemid BridgeDb">BridgeDb: hmdbid -> pubchemid</option>
        <option value="hmdbid wikidataid BridgeDb">BridgeDb: hmdbid -> wikidataid</option>
        <option value="keggid chebiid BridgeDb">BridgeDb: keggid -> chebiid</option>
        <option value="keggid chemspiderid BridgeDb">BridgeDb: keggid -> chemspiderid</option>
        <option value="keggid hmdbid BridgeDb">BridgeDb: keggid -> hmdbid</option>
        <option value="keggid pubchemid BridgeDb">BridgeDb: keggid -> pubchemid</option>
        <option value="keggid wikidataid BridgeDb">BridgeDb: keggid -> wikidataid</option>
        <option value="pubchemid chebiid BridgeDb">BridgeDb: pubchemid -> chebiid</option>
        <option value="pubchemid chemspiderid BridgeDb">BridgeDb: pubchemid -> chemspiderid</option>
        <option value="pubchemid hmdbid BridgeDb">BridgeDb: pubchemid -> hmdbid</option>
        <option value="pubchemid keggid BridgeDb">BridgeDb: pubchemid -> keggid</option>
        <option value="pubchemid wikidataid BridgeDb">BridgeDb: pubchemid -> wikidataid</option>
        <option value="wikidataid chebiid BridgeDb">BridgeDb: wikidataid -> chebiid</option>
        <option value="wikidataid chemspiderid BridgeDb">BridgeDb: wikidataid -> chemspiderid</option>
        <option value="wikidataid hmdbid BridgeDb">BridgeDb: wikidataid -> hmdbid</option>
        <option value="wikidataid keggid BridgeDb">BridgeDb: wikidataid -> keggid</option>
        <option value="wikidataid pubchemid BridgeDb">BridgeDb: wikidataid -> pubchemid</option>
    </xml>

</macros>