diff uniprot.xml @ 9:468c71dac78a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
author bgruening
date Wed, 22 May 2024 21:18:15 +0000
parents af5eccf83605
children 95fb5712344f
line wrap: on
line diff
--- a/uniprot.xml	Mon Nov 21 22:02:41 2022 +0000
+++ b/uniprot.xml	Wed May 22 21:18:15 2024 +0000
@@ -1,197 +1,824 @@
-<tool id="uniprot" name="UniProt" version="0.4">
+<tool id="uniprot" name="UniProt" version="0.5" profile="23.1">
     <description>ID mapping and retrieval</description>
-    <macros>
-         <import>macros.xml</import>
-    </macros>
     <requirements>
         <requirement type="package" version="2.25.1">requests</requirement>
     </requirements>
     <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command>
     <command detect_errors="aggressive"><![CDATA[
-
         cut -f ${id_column} '$infile' > id_file.tabular &&
 
-        '$__tool_directory__/uniprot.py'
-
+        python '$__tool_directory__/uniprot.py'
         #if $tool.tool_choice == "retrieve":
             retrieve -f $tool.format id_file.tabular ./output
         #elif $tool.tool_choice == "map":
             map
-
-            #if $tool.from.category_FROM == "uniprot"
-                '${tool.from.db_uniprot_FROM}'
-            #elif $tool.from.category_FROM == "oseqdb"
-                ${tool.from.db_oseqdb}
-            #elif $tool.from.category_FROM == "3Dstrdb"
-                ${tool.from.db_3Dstrdb}
-            #elif $tool.from.category_FROM == "ppidb"
-                ${tool.from.db_ppidb}
-            #elif $tool.from.category_FROM == "chemistry"
-                ${tool.from.db_chemistry}
-            #elif $tool.from.category_FROM == "protfgdb"
-                ${tool.from.db_protfgdb}
-            #elif $tool.from.category_FROM == "polymorphismANDmutation"
-                ${tool.from.db_polymorphismANDmutation}
-            #elif $tool.from.category_FROM == "2DgelDB"
-                ${tool.from.db_2DgelDB}
-            #elif $tool.from.category_FROM == "ProtocolsMaterialsDB"
-                ${tool.from.db_ProtocolsMaterialsDB}
-            #elif $tool.from.category_FROM == "GenomeAnnotationDB"
-                ${tool.from.db_GenomeAnnotationDB}
-            #elif $tool.from.category_FROM == "OrganismSpecificGeneDB"
-                ${tool.from.db_OrganismSpecificGeneDB}
-            #elif $tool.from.category_FROM == "phylogenomic"
-                ${tool.from.db_phylogenomic}
-            #elif $tool.from.category_FROM == "EnzymePathwayDB"
-                ${tool.from.db_EnzymePathwayDB}
-            #elif $tool.from.category_FROM == "GeneExpression"
-                ${tool.from.db_GeneExpression}
-            #elif $tool.from.category_FROM == "other"
-                ${tool.from.db_other}
-            #end if
-
-            #if $tool.to.category_TO == "uniprot"
-                ${tool.to.db_uniprot_TO}
-            #elif $tool.to.category_TO == "oseqdb"
-                ${tool.to.db_oseqdb}
-            #elif $tool.to.category_TO == "3Dstrdb"
-                ${tool.to.db_3Dstrdb}
-            #elif $tool.to.category_TO == "ppidb"
-                ${tool.to.db_ppidb}
-            #elif $tool.to.category_TO == "chemistry"
-                ${tool.to.db_chemistry}
-            #elif $tool.to.category_TO == "protfgdb"
-                ${tool.to.db_protfgdb}
-            #elif $tool.to.category_TO == "polymorphismANDmutation"
-                ${tool.to.db_polymorphismANDmutation}
-            #elif $tool.to.category_TO == "2DgelDB"
-                ${tool.to.db_2DgelDB}
-            #elif $tool.to.category_TO == "ProtocolsMaterialsDB"
-                ${tool.to.db_ProtocolsMaterialsDB}
-            #elif $tool.to.category_TO == "GenomeAnnotationDB"
-                ${tool.to.db_GenomeAnnotationDB}
-            #elif $tool.to.category_TO == "OrganismSpecificGeneDB"
-                ${tool.to.db_OrganismSpecificGeneDB}
-            #elif $tool.to.category_TO == "phylogenomic"
-                ${tool.to.db_phylogenomic}
-            #elif $tool.to.category_TO == "EnzymePathwayDB"
-                ${tool.to.db_EnzymePathwayDB}
-            #elif $tool.to.category_TO == "GeneExpression"
-                ${tool.to.db_GeneExpression}
-            #elif $tool.to.category_TO == "other"
-                ${tool.to.db_other}
-            #end if
-
+            --format tsv
+            "$from_cond.from"
+            "$from_cond.to"
             id_file.tabular
             ./output
         #end if
-
     ]]></command>
     <inputs>
         <param name="infile" type="data" format="tabular" label="Input file with IDs"
             help="One ID in each line."/>
         <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/>
-
         <conditional name="tool">
             <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help="">
                 <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option>
                 <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option>
             </param>
             <when value="map">
-                <conditional name="from">
-                    <expand macro="macro-category_FROM"/>
-                    <when value="uniprot">
-                        <expand macro="macro-db_uniprot_FROM"/>
-                    </when>
-                    <when value="oseqdb">
-                        <expand macro="macro-db_oseqdb"/>
-                    </when>
-                    <when value="3Dstrdb">
-                        <expand macro="macro-db_3Dstrdb"/>
-                    </when>
-                    <when value="ppidb">
-                        <expand macro="macro-db_ppidb"/>
-                    </when>
-                    <when value="chemistry">
-                        <expand macro="macro-db_chemistry"/>
-                    </when>
-                    <when value="protfgdb">
-                        <expand macro="macro-db_protfgdb"/>
-                    </when>
-                    <when value="polymorphismANDmutation">
-                        <expand macro="macro-db_polymorphismANDmutation"/>
+                <!-- conditional auto generated with python tools/uniprot_rest_interface/uniprot.py menu -->
+                <conditional name="from_cond">
+                    <param name="from" type="select" label="Source database:">
+                        <option value="UniProtKB_AC-ID">UniProt - UniProtKB AC/ID</option>
+                        <option value="UniParc">UniProt - UniParc</option>
+                        <option value="UniRef50">UniProt - UniRef50</option>
+                        <option value="UniRef90">UniProt - UniRef90</option>
+                        <option value="UniRef100">UniProt - UniRef100</option>
+                        <option value="Gene_Name">UniProt - Gene Name</option>
+                        <option value="CRC64">UniProt - CRC64</option>
+                        <option value="CCDS">Sequence DBs - CCDS</option>
+                        <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option>
+                        <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option>
+                        <option value="GI_number">Sequence DBs - GI number</option>
+                        <option value="PIR">Sequence DBs - PIR</option>
+                        <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option>
+                        <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option>
+                        <option value="PDB">3D structure DBs - PDB</option>
+                        <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option>
+                        <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option>
+                        <option value="DIP">Protein-protein interaction DBs - DIP</option>
+                        <option value="STRING">Protein-protein interaction DBs - STRING</option>
+                        <option value="ChEMBL">Chemistry - ChEMBL</option>
+                        <option value="DrugBank">Chemistry - DrugBank</option>
+                        <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option>
+                        <option value="SwissLipids">Chemistry - SwissLipids</option>
+                        <option value="Allergome">Protein family/group DBs - Allergome</option>
+                        <option value="CLAE">Protein family/group DBs - CLAE</option>
+                        <option value="ESTHER">Protein family/group DBs - ESTHER</option>
+                        <option value="MEROPS">Protein family/group DBs - MEROPS</option>
+                        <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option>
+                        <option value="REBASE">Protein family/group DBs - REBASE</option>
+                        <option value="TCDB">Protein family/group DBs - TCDB</option>
+                        <option value="GlyConnect">PTM DBs - GlyConnect</option>
+                        <option value="BioMuta">Genetic variation DBs - BioMuta</option>
+                        <option value="DMDM">Genetic variation DBs - DMDM</option>
+                        <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option>
+                        <option value="CPTAC">Proteomic DBs - CPTAC</option>
+                        <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option>
+                        <option value="DNASU">Protocols and materials DBs - DNASU</option>
+                        <option value="Ensembl">Genome annotation DBs - Ensembl</option>
+                        <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option>
+                        <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option>
+                        <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option>
+                        <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option>
+                        <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option>
+                        <option value="GeneID">Genome annotation DBs - GeneID</option>
+                        <option value="KEGG">Genome annotation DBs - KEGG</option>
+                        <option value="PATRIC">Genome annotation DBs - PATRIC</option>
+                        <option value="UCSC">Genome annotation DBs - UCSC</option>
+                        <option value="WBParaSite">Genome annotation DBs - WBParaSite</option>
+                        <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option>
+                        <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option>
+                        <option value="Araport">Organism-specific DBs - Araport</option>
+                        <option value="CGD">Organism-specific DBs - CGD</option>
+                        <option value="ConoServer">Organism-specific DBs - ConoServer</option>
+                        <option value="dictyBase">Organism-specific DBs - dictyBase</option>
+                        <option value="EchoBASE">Organism-specific DBs - EchoBASE</option>
+                        <option value="euHCVdb">Organism-specific DBs - euHCVdb</option>
+                        <option value="FlyBase">Organism-specific DBs - FlyBase</option>
+                        <option value="GeneCards">Organism-specific DBs - GeneCards</option>
+                        <option value="GeneReviews">Organism-specific DBs - GeneReviews</option>
+                        <option value="HGNC">Organism-specific DBs - HGNC</option>
+                        <option value="LegioList">Organism-specific DBs - LegioList</option>
+                        <option value="Leproma">Organism-specific DBs - Leproma</option>
+                        <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option>
+                        <option value="MGI">Organism-specific DBs - MGI</option>
+                        <option value="MIM">Organism-specific DBs - MIM</option>
+                        <option value="neXtProt">Organism-specific DBs - neXtProt</option>
+                        <option value="OpenTargets">Organism-specific DBs - OpenTargets</option>
+                        <option value="Orphanet">Organism-specific DBs - Orphanet</option>
+                        <option value="PharmGKB">Organism-specific DBs - PharmGKB</option>
+                        <option value="PomBase">Organism-specific DBs - PomBase</option>
+                        <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option>
+                        <option value="RGD">Organism-specific DBs - RGD</option>
+                        <option value="SGD">Organism-specific DBs - SGD</option>
+                        <option value="TubercuList">Organism-specific DBs - TubercuList</option>
+                        <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option>
+                        <option value="VGNC">Organism-specific DBs - VGNC</option>
+                        <option value="WormBase">Organism-specific DBs - WormBase</option>
+                        <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option>
+                        <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option>
+                        <option value="Xenbase">Organism-specific DBs - Xenbase</option>
+                        <option value="ZFIN">Organism-specific DBs - ZFIN</option>
+                        <option value="eggNOG">Phylogenomic DBs - eggNOG</option>
+                        <option value="GeneTree">Phylogenomic DBs - GeneTree</option>
+                        <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option>
+                        <option value="OMA">Phylogenomic DBs - OMA</option>
+                        <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option>
+                        <option value="TreeFam">Phylogenomic DBs - TreeFam</option>
+                        <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option>
+                        <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option>
+                        <option value="Reactome">Enzyme and pathway DBs - Reactome</option>
+                        <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option>
+                        <option value="ChiTaRS">Miscellaneous - ChiTaRS</option>
+                        <option value="GeneWiki">Miscellaneous - GeneWiki</option>
+                        <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option>
+                        <option value="PHI-base">Miscellaneous - PHI-base</option>
+                        <option value="CollecTF">Gene expression DBs - CollecTF</option>
+                        <option value="DisProt">Family and domain DBs - DisProt</option>
+                        <option value="IDEAL">Family and domain DBs - IDEAL</option>
+                    </param>
+                    <when value="UniProtKB_AC-ID">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="CCDS">Sequence DBs - CCDS</option>
+                            <option value="PIR">Sequence DBs - PIR</option>
+                            <option value="PDB">3D structure DBs - PDB</option>
+                            <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option>
+                            <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option>
+                            <option value="DIP">Protein-protein interaction DBs - DIP</option>
+                            <option value="STRING">Protein-protein interaction DBs - STRING</option>
+                            <option value="ChEMBL">Chemistry - ChEMBL</option>
+                            <option value="DrugBank">Chemistry - DrugBank</option>
+                            <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option>
+                            <option value="SwissLipids">Chemistry - SwissLipids</option>
+                            <option value="Allergome">Protein family/group DBs - Allergome</option>
+                            <option value="ESTHER">Protein family/group DBs - ESTHER</option>
+                            <option value="MEROPS">Protein family/group DBs - MEROPS</option>
+                            <option value="CLAE">Protein family/group DBs - CLAE</option>
+                            <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option>
+                            <option value="REBASE">Protein family/group DBs - REBASE</option>
+                            <option value="TCDB">Protein family/group DBs - TCDB</option>
+                            <option value="GlyConnect">PTM DBs - GlyConnect</option>
+                            <option value="BioMuta">Genetic variation DBs - BioMuta</option>
+                            <option value="DMDM">Genetic variation DBs - DMDM</option>
+                            <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option>
+                            <option value="CPTAC">Proteomic DBs - CPTAC</option>
+                            <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option>
+                            <option value="DNASU">Protocols and materials DBs - DNASU</option>
+                            <option value="Ensembl">Genome annotation DBs - Ensembl</option>
+                            <option value="GeneID">Genome annotation DBs - GeneID</option>
+                            <option value="KEGG">Genome annotation DBs - KEGG</option>
+                            <option value="PATRIC">Genome annotation DBs - PATRIC</option>
+                            <option value="UCSC">Genome annotation DBs - UCSC</option>
+                            <option value="WBParaSite">Genome annotation DBs - WBParaSite</option>
+                            <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option>
+                            <option value="Araport">Organism-specific DBs - Araport</option>
+                            <option value="CGD">Organism-specific DBs - CGD</option>
+                            <option value="ConoServer">Organism-specific DBs - ConoServer</option>
+                            <option value="dictyBase">Organism-specific DBs - dictyBase</option>
+                            <option value="EchoBASE">Organism-specific DBs - EchoBASE</option>
+                            <option value="euHCVdb">Organism-specific DBs - euHCVdb</option>
+                            <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option>
+                            <option value="FlyBase">Organism-specific DBs - FlyBase</option>
+                            <option value="GeneCards">Organism-specific DBs - GeneCards</option>
+                            <option value="GeneReviews">Organism-specific DBs - GeneReviews</option>
+                            <option value="HGNC">Organism-specific DBs - HGNC</option>
+                            <option value="LegioList">Organism-specific DBs - LegioList</option>
+                            <option value="Leproma">Organism-specific DBs - Leproma</option>
+                            <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option>
+                            <option value="MGI">Organism-specific DBs - MGI</option>
+                            <option value="MIM">Organism-specific DBs - MIM</option>
+                            <option value="neXtProt">Organism-specific DBs - neXtProt</option>
+                            <option value="OpenTargets">Organism-specific DBs - OpenTargets</option>
+                            <option value="Orphanet">Organism-specific DBs - Orphanet</option>
+                            <option value="PharmGKB">Organism-specific DBs - PharmGKB</option>
+                            <option value="PomBase">Organism-specific DBs - PomBase</option>
+                            <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option>
+                            <option value="RGD">Organism-specific DBs - RGD</option>
+                            <option value="SGD">Organism-specific DBs - SGD</option>
+                            <option value="TubercuList">Organism-specific DBs - TubercuList</option>
+                            <option value="VGNC">Organism-specific DBs - VGNC</option>
+                            <option value="WormBase">Organism-specific DBs - WormBase</option>
+                            <option value="Xenbase">Organism-specific DBs - Xenbase</option>
+                            <option value="ZFIN">Organism-specific DBs - ZFIN</option>
+                            <option value="eggNOG">Phylogenomic DBs - eggNOG</option>
+                            <option value="GeneTree">Phylogenomic DBs - GeneTree</option>
+                            <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option>
+                            <option value="OMA">Phylogenomic DBs - OMA</option>
+                            <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option>
+                            <option value="TreeFam">Phylogenomic DBs - TreeFam</option>
+                            <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option>
+                            <option value="Reactome">Enzyme and pathway DBs - Reactome</option>
+                            <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option>
+                            <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option>
+                            <option value="ChiTaRS">Miscellaneous - ChiTaRS</option>
+                            <option value="GeneWiki">Miscellaneous - GeneWiki</option>
+                            <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option>
+                            <option value="PHI-base">Miscellaneous - PHI-base</option>
+                            <option value="CollecTF">Gene expression DBs - CollecTF</option>
+                            <option value="IDEAL">Family and domain DBs - IDEAL</option>
+                            <option value="DisProt">Family and domain DBs - DisProt</option>
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                            <option value="UniParc">UniProt - UniParc</option>
+                            <option value="UniRef50">UniProt - UniRef50</option>
+                            <option value="UniRef90">UniProt - UniRef90</option>
+                            <option value="UniRef100">UniProt - UniRef100</option>
+                            <option value="Gene_Name">UniProt - Gene Name</option>
+                            <option value="CRC64">UniProt - CRC64</option>
+                            <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option>
+                            <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option>
+                            <option value="GI_number">Sequence DBs - GI number</option>
+                            <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option>
+                            <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option>
+                            <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option>
+                            <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option>
+                            <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option>
+                            <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option>
+                            <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option>
+                            <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option>
+                            <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option>
+                            <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option>
+                        </param>
                     </when>
-                    <when value="2DgelDB">
-                        <expand macro="macro-db_2DgelDB"/>
+                    <when value="UniParc">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                            <option value="UniParc">UniProt - UniParc</option>
+                        </param>
+                    </when>
+                    <when value="UniRef50">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                            <option value="UniRef50">UniProt - UniRef50</option>
+                        </param>
+                    </when>
+                    <when value="UniRef90">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                            <option value="UniRef90">UniProt - UniRef90</option>
+                        </param>
                     </when>
-                    <when value="ProtocolsMaterialsDB">
-                        <expand macro="macro-db_ProtocolsMaterialsDB"/>
+                    <when value="UniRef100">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                            <option value="UniRef100">UniProt - UniRef100</option>
+                        </param>
+                    </when>
+                    <when value="Gene_Name">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="CRC64">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="CCDS">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="GenomeAnnotationDB">
-                        <expand macro="macro-db_GenomeAnnotationDB"/>
+                    <when value="EMBL-GenBank-DDBJ">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="EMBL-GenBank-DDBJ_CDS">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GI_number">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PIR">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="OrganismSpecificGeneDB">
-                        <expand macro="macro-db_OrganismSpecificGeneDB"/>
+                    <when value="RefSeq_Nucleotide">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="RefSeq_Protein">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PDB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="BioGRID">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="phylogenomic">
-                        <expand macro="macro-db_phylogenomic"/>
+                    <when value="ComplexPortal">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="DIP">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="STRING">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="ChEMBL">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="EnzymePathwayDB">
-                        <expand macro="macro-db_EnzymePathwayDB"/>
+                    <when value="DrugBank">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GuidetoPHARMACOLOGY">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="SwissLipids">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Allergome">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="GeneExpression">
-                        <expand macro="macro-db_GeneExpression"/>
+                    <when value="CLAE">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="ESTHER">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="MEROPS">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PeroxiBase">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="other">
-                        <expand macro="macro-db_other"/>
+                    <when value="REBASE">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="TCDB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GlyConnect">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="BioMuta">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                </conditional>
-                <conditional name="to">
-                    <expand macro="macro-category_TO"/>
-                    <when value="uniprot">
-                        <expand macro="macro-db_uniprot_TO"/>
+                    <when value="DMDM">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="World-2DPAGE">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="CPTAC">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="ProteomicsDB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="DNASU">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Ensembl">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Ensembl_Genomes">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Ensembl_Genomes_Protein">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="oseqdb">
-                        <expand macro="macro-db_oseqdb"/>
+                    <when value="Ensembl_Genomes_Transcript">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Ensembl_Protein">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Ensembl_Transcript">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GeneID">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="3Dstrdb">
-                        <expand macro="macro-db_3Dstrdb"/>
+                    <when value="KEGG">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PATRIC">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="UCSC">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="WBParaSite">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="ppidb">
-                        <expand macro="macro-db_ppidb"/>
+                    <when value="WBParaSite_Transcript-Protein">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="ArachnoServer">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Araport">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="CGD">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="chemistry">
-                        <expand macro="macro-db_chemistry"/>
+                    <when value="ConoServer">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="dictyBase">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="EchoBASE">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="euHCVdb">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="protfgdb">
-                        <expand macro="macro-db_protfgdb"/>
+                    <when value="FlyBase">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GeneCards">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GeneReviews">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="HGNC">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="polymorphismANDmutation">
-                        <expand macro="macro-db_polymorphismANDmutation"/>
+                    <when value="LegioList">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Leproma">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="MaizeGDB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="MGI">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="MIM">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="2DgelDB">
-                        <expand macro="macro-db_2DgelDB"/>
+                    <when value="neXtProt">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="OpenTargets">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Orphanet">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PharmGKB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="ProtocolsMaterialsDB">
-                        <expand macro="macro-db_ProtocolsMaterialsDB"/>
+                    <when value="PomBase">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PseudoCAP">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="RGD">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="SGD">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="GenomeAnnotationDB">
-                        <expand macro="macro-db_GenomeAnnotationDB"/>
+                    <when value="TubercuList">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="VEuPathDB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="VGNC">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="WormBase">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="OrganismSpecificGeneDB">
-                        <expand macro="macro-db_OrganismSpecificGeneDB"/>
+                    <when value="WormBase_Protein">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="WormBase_Transcript">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="Xenbase">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="ZFIN">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="phylogenomic">
-                        <expand macro="macro-db_phylogenomic"/>
+                    <when value="eggNOG">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GeneTree">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="HOGENOM">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="OMA">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="EnzymePathwayDB">
-                        <expand macro="macro-db_EnzymePathwayDB"/>
+                    <when value="OrthoDB">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="TreeFam">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="BioCyc">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PlantReactome">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="GeneExpression">
-                        <expand macro="macro-db_GeneExpression"/>
+                    <when value="Reactome">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="UniPathway">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="ChiTaRS">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="GeneWiki">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
-                    <when value="other">
-                        <expand macro="macro-db_other"/>
+                    <when value="GenomeRNAi">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="PHI-base">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="CollecTF">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="DisProt">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
+                    </when>
+                    <when value="IDEAL">
+                        <param name="to" type="select" label="Target database:">
+                            <option value="UniProtKB">UniProt - UniProtKB</option>
+                            <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
+                        </param>
                     </when>
                 </conditional>
             </when>
@@ -206,58 +833,54 @@
     </inputs>
     <outputs>
             <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
-                label="${tool.name} on ${on_string} (retrieve output)">
+                label="${tool.name} on ${on_string}: fasta">
                 <filter>tool['tool_choice'] == 'retrieve'</filter>
                 <filter>tool['format'] == 'fasta'</filter>
             </data>
             <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
-                label="${tool.name} on ${on_string} (retrieve output)">
+                label="${tool.name} on ${on_string}: gff">
                 <filter>tool['tool_choice'] == 'retrieve'</filter>
                 <filter>tool['format'] == 'gff'</filter>
             </data>
             <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
-                label="${tool.name} on ${on_string} (retrieve output)">
+                label="${tool.name} on ${on_string}: txt">
                	<filter>tool['tool_choice'] == 'retrieve'</filter>
                 <filter>tool['format'] == 'txt'</filter>
             </data>
             <data name="outfile_map" format="tabular" from_work_dir="./output"
-                label="${tool.name} on ${on_string} (map output)">
+                label="${tool.name} on ${on_string}: mapping">
                 <filter>tool['tool_choice'] == 'map'</filter>
             </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
             <param name="id_column" value="c1"/>
             <param name="format" value="fasta"/>
             <param name="tool_choice" value="retrieve"/>
             <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
             <param name="id_column" value="c1"/>
             <param name="format" value="gff"/>
             <param name="tool_choice" value="retrieve"/>
             <output name="outfile_retrieve_gff" file="test2_retrieve.gff" ftype="gff" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
             <param name="id_column" value="c1"/>
             <param name="tool_choice" value="map"/>
-            <param name="category_FROM" value="uniprot"/>
-            <param name="db_uniprot_FROM" value="ID"/>
-            <param name="category_TO" value="uniprot"/>
-            <param name="db_uniprot_TO" value="GENENAME"/>
+            <param name="from" value="UniProtKB_AC-ID"/>
+            <param name="to" value="Gene_Name"/>
             <output name="outfile_map" file="test1_map.tab" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" value="id_map_refseq.txt" ftype="tabular"/>
             <param name="id_column" value="c1"/>
             <param name="tool_choice" value="map"/>
-            <param name="category_FROM" value="oseqdb"/>
-            <param name="db_oseqdb" value="REFSEQ_NT_ID"/>
-            <param name="category_TO" value="uniprot"/>
-            <param name="db_uniprot_TO" value="ID"/>
+            <param name="from" value="RefSeq_Nucleotide"/>
+            <param name="to" value="UniProtKB"/>
             <output name="outfile_map" file="test2_map.tab" ftype="tabular"/>
         </test>
     </tests>