annotate macros.xml @ 1:cd2a41c65447 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489

<macros>
<token name="@EXECUTABLE@">1.0</token>
    <macro name="macro-category_FROM">
            <param name="category_FROM" type="select" label="Choose your database category (FROM):"
                help="Select a databse from which your ids are coming from">
                <option value="uniprot">UniProt</option>
                <option value="oseqdb">Other sequence databases</option>
                <option value="3Dstrdb">3D structure databases</option>
                <option value="ppidb">Protein-protein interaction databases</option>
                <option value="chemistry">Chemistry</option>
                <option value="protfgdb">Protein family/group databases</option>
                <option value="polymorphismANDmutation">Polymorphism and mutation databases</option>
                <option value="2DgelDB">2D gel databases</option>
                <option value="ProtocolsMaterialsDB">Protocols and materials databases</option>
                <option value="GenomeAnnotationDB">Genome annotation databases</option>
                <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option>
                <option value="phylogenomic">Phylogenomic databases</option>
                <option value="EnzymePathwayDB">Enzyme and pathway databases</option>
                <option value="GeneExpression">Gene expression databases</option>
                <option value="other">Other</option>
            </param>
        </macro>
        <macro name="macro-category_TO">
            <param name="category_TO" type="select" label="Choose your database category (TO):"
                help="Select a database which will be used for mapping">
                <option value="uniprot">UniProt</option>
                <option value="oseqdb">Other sequence databases</option>
                <option value="3Dstrdb">3D structure databases</option>
                <option value="ppidb">Protein-protein interaction databases</option>
                <option value="chemistry">Chemistry</option>
                <option value="protfgdb">Protein family/group databases</option>
                <option value="polymorphismANDmutation">Polymorphism and mutation databases</option>
                <option value="2DgelDB">2D gel databases</option>
                <option value="ProtocolsMaterialsDB">Protocols and materials databases</option>
                <option value="GenomeAnnotationDB">Genome annotation databases</option>
                <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option>
                <option value="phylogenomic">Phylogenomic databases</option>
                <option value="EnzymePathwayDB">Enzyme and pathway databases</option>
                <option value="GeneExpression">Gene expression databases</option>
                <option value="other">Other</option>
            </param>
        </macro>
        <macro name="macro-db_uniprot_FROM">
            <param name="db_uniprot_FROM" type="select" label="Choose a database:"
                                help="">
                                <option value="ACC+ID">UniProtKB AC/ID</option>
                                <option value="ACC">UniProtKB AC</option>
                                <option value="ID">UniProtKB ID</option>
                                <option value="ACC">UniProtKB AC</option>
                                <option value="UPARC">UniParc</option>
                                <option value="NF50">UniRef50</option>
                                <option value="NF90">UniRef90</option>
                                <option value="NF100">UniRef100</option>
                                <option value="GENENAME">Gene name</option>
            </param>
        </macro>
        <macro name="macro-db_uniprot_TO">
            <param name="db_uniprot_TO" type="select" label="Choose a database:"
                                help="">
                                <option value="ACC">UniProtKB AC</option>
                                <option value="ID">UniProtKB ID</option>
                                <option value="ACC">UniProtKB AC</option>
                                <option value="UPARC">UniParc</option>
                                <option value="NF50">UniRef50</option>
                                <option value="NF90">UniRef90</option>
                                <option value="NF100">UniRef100</option>
                                <option value="GENENAME">Gene name</option>
            </param>
        </macro>
        <macro name="macro-db_oseqdb">
            <param name="db_oseqdb" type="select" label="Choose a database:"
                help="">
                <option value="EMBL_ID">EMBL/GenBank/DDBJ</option>
                <option value="EMBL">EMBL/GenBank/DDBJ CDS</option>
                <option value="PIR">PIR</option>

                <option value="UNIGENE_ID">UniParc</option>
                <option value="P_ENTREZGENEID">Entrez Gene (GeneID)</option>
                <option value="P_GI">GI number</option>
                <option value="P_REFSEQ_AC">RefSeq Protein</option>
                <option value="REFSEQ_NT_ID">RefSeq Nucleotide</option>
            </param>
        </macro>
        <macro name="macro-db_3Dstrdb">
            <param name="db_3Dstrdb" type="select" label="Choose a database:"
                help="">
                <option value="PDB_ID">PDB</option>
                <option value="DISPROT_ID">DisProt</option>
            </param>
        </macro>
        <macro name="macro-db_ppidb">
            <param name="db_ppidb" type="select" label="Choose a database:"
                help="">
                <option value="BIOGRID_ID">BioGrid</option>
                <option value="DIP_ID">DIP</option>
                <option value="MINT_ID">MINT</option>
                <option value="STRING_ID">STRING</option>
            </param>
        </macro>
        <macro name="macro-db_chemistry">
            <param name="db_chemistry" type="select" label="Choose a database:"
                help="">
                <option value="CHEMBL_ID">ChEMBL</option>
                <option value="DrugBank_ID">DrugBank</option>
                <option value="GUIDETOPHARMACOLOGY_ID">GuidetoPHARMACOLOGY</option>
            </param>
        </macro>
        <macro name="macro-db_protfgdb">
            <param name="db_protfgdb" type="select" label="Choose a database:"
                help="">
                <option value="ALLERGOME_ID">Allergome</option>
                <option value="MEROPS_ID">MEROPS</option>
                <option value="MYCOCLAP_ID">mycoCLAP</option>
                <option value="PEROXIBASE_ID">PeroxiBase</option>
                <option value="REBASE_ID">REBASE</option>
                <option value="TCDB_ID">TCDB</option>
            </param>
        </macro>
        <macro name="macro-db_polymorphismANDmutation">
            <param name="db_polymorphismANDmutation" type="select" label="Choose a database:"
                help="">
                <option value="DMDM_ID">DMDM</option>
            </param>
        </macro>
        <macro name="macro-db_2DgelDB">
            <param name="db_2DgelDB" type="select" label="Choose a database:"
                help="">
                <option value="WORLD_2DPAGE_ID">World-2DPAGE</option>
            </param>
        </macro>
        <macro name="macro-db_ProtocolsMaterialsDB">
            <param name="db_ProtocolsMaterialsDB" type="select" label="Choose a database:"
                help="">
                <option value="DNASU_ID">DNASU</option>
            </param>
        </macro>
        <macro name="macro-db_GenomeAnnotationDB">
            <param name="db_GenomeAnnotationDB" type="select" label="Choose a database:"
                help="">
                <option value="ENSEMBL_ID">Ensembl</option>
                <option value="ENSEMBL_PRO_ID">Ensembl Protein</option>
                <option value="ENSEMBL_TRS_ID">Ensembl Transcript</option>
                <option value="ENSEMBLGENOME_ID">Ensembl Genomes</option>
                <option value="ENSEMBLGENOME_PRO_ID">Ensembl Genomes Protein</option>
                <option value="ENSEMBLGENOME_TRS_ID">Ensembl Genomes Transcript</option>
                <option value="P_ENTREZGENEID">GeneID</option>
                <option value="KEGG_ID">KEGG</option>
                <option value="PATRIC_ID">PATRIC</option>
                <option value="UCSC_ID">UCSC</option>
                <option value="VECTORBASE_ID">VectorBase</option>
            </param>
        </macro>
        <macro name="macro-db_OrganismSpecificGeneDB">
            <param name="db_OrganismSpecificGeneDB" type="select" label="Choose a database:"
                help="">
                <option value="ARACHNOSERVER_ID">ArachnoServer</option>
                <option value="CGD">CGD</option>
                <option value="CONOSERVER_ID">ConoServer</option>
                <option value="DICTYBASE_ID">dictyBase</option>
                <option value="ECHOBASE_ID">EchoBASE</option>
                <option value="ECOGENE_ID">EcoGene</option>
                <option value="EUHCVDB_ID">euHCVdb</option>
                <option value="EUPATHDB_ID">EuPathDB</option>
                <option value="FLYBASE_ID">FlyBase</option>
                <option value="GENECARDS_ID">GeneCards</option>
                <option value="GENEFARM_ID">GeneFarm</option>
                <option value="GENOLIST_ID">GenoList</option>
                <option value="H_INVDB_ID">H-InvDB</option>
                <option value="HGNC_ID">HGNC</option>
                <option value="HPA_ID">HPA</option>
                <option value="LEGIOLIST_ID">LegioList</option>
                <option value="MAIZEGDB_ID">MaizeGDB</option>
                <option value="MIM_ID">MIM</option>
                <option value="MGI_ID">MGI</option>
                <option value="NEXTPROT_ID">neXtProt</option>
                <option value="ORPHANET_ID">Orphanet</option>
                <option value="PHARMGKB_ID">PharmGKB</option>
                <option value="POMBASE_ID">PomBase</option>
                <option value="PSEUDOCAP_ID">PseudoCAP</option>
                <option value="RGD_ID">RGD</option>
                <option value="SGD_ID">SGD</option>
                <option value="TAIR_ID">TAIR</option>
                <option value="TUBERCULIST_ID">TubercuList</option>
                <option value="WORMBASE_ID">WormBase</option>
                <option value="WORMBASE_TRS_ID">WormBase Transcript</option>
                <option value="WORMBASE_PRO_ID">WormBase Protein</option>
                <option value="XENBASE_ID">Xenbase</option>
                <option value="ZFIN_ID">ZFIN</option>
            </param>
        </macro>
        <macro name="macro-db_phylogenomic">
            <param name="db_phylogenomic" type="select" label="Choose a database:"
                help="">
                <option value="EGGNOG_ID">eggNOG</option>
                <option value="GENETREE_ID">GeneTree</option>
                <option value="HOGENOM_ID">HOGENOM</option>
                <option value="HOVERGEN_ID">HOVERGEN</option>
                <option value="KO_ID">KO</option>
                <option value="OMA_ID">OMA</option>
                <option value="ORTHODB_ID">OrthoDB</option>
                <option value="PROTCLUSTDB_ID">ProtClustDB</option>
                <option value="TREEFAM_ID">TreeFam</option>
            </param>
        </macro>
        <macro name="macro-db_EnzymePathwayDB">
            <param name="db_EnzymePathwayDB" type="select" label="Choose a database:"
                help="">
                <option value="BIOCYC_ID">BioCyc</option>
                <option value="REACTOME_ID">Reactome</option>
                <option value="UNIPATHWAY_ID">UniPathWay</option>
            </param>
        </macro>
        <macro name="macro-db_GeneExpression">
            <param name="db_GeneExpression" type="select" label="Choose a database:"
                help="">
                <option value="CLEANEX_ID">CleanEx</option>
            </param>
        </macro>
        <macro name="macro-db_other">
            <param name="db_other" type="select" label="Choose a database:"
                help="">
                <option value="CHITARS_ID">ChiTaRS</option>
                <option value="GENOMERNAI_ID">GenomeRNAi</option>
                <option value="GENEWIKI_ID">GeneWiki</option>
                <option value="NEXTBIO_ID">NextBio</option>
            </param>
        </macro>
</macros>