Mercurial > repos > recetox > msmetaenhancer

view macros.xml @ 0:ce612a11b455 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
author recetox
date Tue, 22 Mar 2022 15:33:37 +0000
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children b50c2e941cae
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<macros>
    <token name="@TOOL_VERSION@">0.2.0</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="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
                name="RECETOX MUNI" />
        </creator>
    </xml>

    <token name="@HELP@">
        <![CDATA[
        MSMetaEnhancer will fetch and update various metadata included in your spectra .msp 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/.
    ]]>
    </token>

    <xml name="job_options">
        <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</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 casno NLM">NLM: compound_name -> casno</option>
        <option value="compound_name formula NLM">NLM: compound_name -> formula</option>
        <option value="compound_name inchikey NLM">NLM: compound_name -> inchikey</option>
        <option value="inchikey casno NLM">NLM: inchikey -> casno</option>
        <option value="inchikey compound_name NLM">NLM: inchikey -> compound_name</option>
        <option value="inchikey formula NLM">NLM: inchikey -> formula</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 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 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 pubchemid BridgeDB">BridgeDB: hmdbid -> pubchemid</option>
        <option value="hmdbid wikidataid BridgeDB">BridgeDB: hmdbid -> 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 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 pubchemid BridgeDB">BridgeDB: wikidataid -> pubchemid</option>
    </xml>

</macros>