Mercurial > repos > bgruening > uniprot_rest_interface

comparison uniprot.xml @ 9:468c71dac78a draft

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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
comparison
equal deleted inserted replaced
8:af5eccf83605 9:468c71dac78a
1 <tool id="uniprot" name="UniProt" version="0.4"> 1 <tool id="uniprot" name="UniProt" version="0.5" profile="23.1">
2 <description>ID mapping and retrieval</description> 2 <description>ID mapping and retrieval</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements> 3 <requirements>
7 <requirement type="package" version="2.25.1">requests</requirement> 4 <requirement type="package" version="2.25.1">requests</requirement>
8 </requirements> 5 </requirements>
9 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> 6 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command>
10 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
11
12 cut -f ${id_column} '$infile' > id_file.tabular && 8 cut -f ${id_column} '$infile' > id_file.tabular &&
13 9
14 '$__tool_directory__/uniprot.py' 10 python '$__tool_directory__/uniprot.py'
15
16 #if $tool.tool_choice == "retrieve": 11 #if $tool.tool_choice == "retrieve":
17 retrieve -f $tool.format id_file.tabular ./output 12 retrieve -f $tool.format id_file.tabular ./output
18 #elif $tool.tool_choice == "map": 13 #elif $tool.tool_choice == "map":
19 map 14 map
20 15 --format tsv
21 #if $tool.from.category_FROM == "uniprot" 16 "$from_cond.from"
22 '${tool.from.db_uniprot_FROM}' 17 "$from_cond.to"
23 #elif $tool.from.category_FROM == "oseqdb"
24 ${tool.from.db_oseqdb}
25 #elif $tool.from.category_FROM == "3Dstrdb"
26 ${tool.from.db_3Dstrdb}
27 #elif $tool.from.category_FROM == "ppidb"
28 ${tool.from.db_ppidb}
29 #elif $tool.from.category_FROM == "chemistry"
30 ${tool.from.db_chemistry}
31 #elif $tool.from.category_FROM == "protfgdb"
32 ${tool.from.db_protfgdb}
33 #elif $tool.from.category_FROM == "polymorphismANDmutation"
34 ${tool.from.db_polymorphismANDmutation}
35 #elif $tool.from.category_FROM == "2DgelDB"
36 ${tool.from.db_2DgelDB}
37 #elif $tool.from.category_FROM == "ProtocolsMaterialsDB"
38 ${tool.from.db_ProtocolsMaterialsDB}
39 #elif $tool.from.category_FROM == "GenomeAnnotationDB"
40 ${tool.from.db_GenomeAnnotationDB}
41 #elif $tool.from.category_FROM == "OrganismSpecificGeneDB"
42 ${tool.from.db_OrganismSpecificGeneDB}
43 #elif $tool.from.category_FROM == "phylogenomic"
44 ${tool.from.db_phylogenomic}
45 #elif $tool.from.category_FROM == "EnzymePathwayDB"
46 ${tool.from.db_EnzymePathwayDB}
47 #elif $tool.from.category_FROM == "GeneExpression"
48 ${tool.from.db_GeneExpression}
49 #elif $tool.from.category_FROM == "other"
50 ${tool.from.db_other}
51 #end if
52
53 #if $tool.to.category_TO == "uniprot"
54 ${tool.to.db_uniprot_TO}
55 #elif $tool.to.category_TO == "oseqdb"
56 ${tool.to.db_oseqdb}
57 #elif $tool.to.category_TO == "3Dstrdb"
58 ${tool.to.db_3Dstrdb}
59 #elif $tool.to.category_TO == "ppidb"
60 ${tool.to.db_ppidb}
61 #elif $tool.to.category_TO == "chemistry"
62 ${tool.to.db_chemistry}
63 #elif $tool.to.category_TO == "protfgdb"
64 ${tool.to.db_protfgdb}
65 #elif $tool.to.category_TO == "polymorphismANDmutation"
66 ${tool.to.db_polymorphismANDmutation}
67 #elif $tool.to.category_TO == "2DgelDB"
68 ${tool.to.db_2DgelDB}
69 #elif $tool.to.category_TO == "ProtocolsMaterialsDB"
70 ${tool.to.db_ProtocolsMaterialsDB}
71 #elif $tool.to.category_TO == "GenomeAnnotationDB"
72 ${tool.to.db_GenomeAnnotationDB}
73 #elif $tool.to.category_TO == "OrganismSpecificGeneDB"
74 ${tool.to.db_OrganismSpecificGeneDB}
75 #elif $tool.to.category_TO == "phylogenomic"
76 ${tool.to.db_phylogenomic}
77 #elif $tool.to.category_TO == "EnzymePathwayDB"
78 ${tool.to.db_EnzymePathwayDB}
79 #elif $tool.to.category_TO == "GeneExpression"
80 ${tool.to.db_GeneExpression}
81 #elif $tool.to.category_TO == "other"
82 ${tool.to.db_other}
83 #end if
84
85 id_file.tabular 18 id_file.tabular
86 ./output 19 ./output
87 #end if 20 #end if
88
89 ]]></command> 21 ]]></command>
90 <inputs> 22 <inputs>
91 <param name="infile" type="data" format="tabular" label="Input file with IDs" 23 <param name="infile" type="data" format="tabular" label="Input file with IDs"
92 help="One ID in each line."/> 24 help="One ID in each line."/>
93 <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/> 25 <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/>
94
95 <conditional name="tool"> 26 <conditional name="tool">
96 <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help=""> 27 <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help="">
97 <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option> 28 <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option>
98 <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option> 29 <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option>
99 </param> 30 </param>
100 <when value="map"> 31 <when value="map">
101 <conditional name="from"> 32 <!-- conditional auto generated with python tools/uniprot_rest_interface/uniprot.py menu -->
102 <expand macro="macro-category_FROM"/> 33 <conditional name="from_cond">
103 <when value="uniprot"> 34 <param name="from" type="select" label="Source database:">
104 <expand macro="macro-db_uniprot_FROM"/> 35 <option value="UniProtKB_AC-ID">UniProt - UniProtKB AC/ID</option>
105 </when> 36 <option value="UniParc">UniProt - UniParc</option>
106 <when value="oseqdb"> 37 <option value="UniRef50">UniProt - UniRef50</option>
107 <expand macro="macro-db_oseqdb"/> 38 <option value="UniRef90">UniProt - UniRef90</option>
108 </when> 39 <option value="UniRef100">UniProt - UniRef100</option>
109 <when value="3Dstrdb"> 40 <option value="Gene_Name">UniProt - Gene Name</option>
110 <expand macro="macro-db_3Dstrdb"/> 41 <option value="CRC64">UniProt - CRC64</option>
111 </when> 42 <option value="CCDS">Sequence DBs - CCDS</option>
112 <when value="ppidb"> 43 <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option>
113 <expand macro="macro-db_ppidb"/> 44 <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option>
114 </when> 45 <option value="GI_number">Sequence DBs - GI number</option>
115 <when value="chemistry"> 46 <option value="PIR">Sequence DBs - PIR</option>
116 <expand macro="macro-db_chemistry"/> 47 <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option>
117 </when> 48 <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option>
118 <when value="protfgdb"> 49 <option value="PDB">3D structure DBs - PDB</option>
119 <expand macro="macro-db_protfgdb"/> 50 <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option>
120 </when> 51 <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option>
121 <when value="polymorphismANDmutation"> 52 <option value="DIP">Protein-protein interaction DBs - DIP</option>
122 <expand macro="macro-db_polymorphismANDmutation"/> 53 <option value="STRING">Protein-protein interaction DBs - STRING</option>
123 </when> 54 <option value="ChEMBL">Chemistry - ChEMBL</option>
124 <when value="2DgelDB"> 55 <option value="DrugBank">Chemistry - DrugBank</option>
125 <expand macro="macro-db_2DgelDB"/> 56 <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option>
126 </when> 57 <option value="SwissLipids">Chemistry - SwissLipids</option>
127 <when value="ProtocolsMaterialsDB"> 58 <option value="Allergome">Protein family/group DBs - Allergome</option>
128 <expand macro="macro-db_ProtocolsMaterialsDB"/> 59 <option value="CLAE">Protein family/group DBs - CLAE</option>
129 </when> 60 <option value="ESTHER">Protein family/group DBs - ESTHER</option>
130 <when value="GenomeAnnotationDB"> 61 <option value="MEROPS">Protein family/group DBs - MEROPS</option>
131 <expand macro="macro-db_GenomeAnnotationDB"/> 62 <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option>
132 </when> 63 <option value="REBASE">Protein family/group DBs - REBASE</option>
133 <when value="OrganismSpecificGeneDB"> 64 <option value="TCDB">Protein family/group DBs - TCDB</option>
134 <expand macro="macro-db_OrganismSpecificGeneDB"/> 65 <option value="GlyConnect">PTM DBs - GlyConnect</option>
135 </when> 66 <option value="BioMuta">Genetic variation DBs - BioMuta</option>
136 <when value="phylogenomic"> 67 <option value="DMDM">Genetic variation DBs - DMDM</option>
137 <expand macro="macro-db_phylogenomic"/> 68 <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option>
138 </when> 69 <option value="CPTAC">Proteomic DBs - CPTAC</option>
139 <when value="EnzymePathwayDB"> 70 <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option>
140 <expand macro="macro-db_EnzymePathwayDB"/> 71 <option value="DNASU">Protocols and materials DBs - DNASU</option>
141 </when> 72 <option value="Ensembl">Genome annotation DBs - Ensembl</option>
142 <when value="GeneExpression"> 73 <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option>
143 <expand macro="macro-db_GeneExpression"/> 74 <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option>
144 </when> 75 <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option>
145 <when value="other"> 76 <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option>
146 <expand macro="macro-db_other"/> 77 <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option>
147 </when> 78 <option value="GeneID">Genome annotation DBs - GeneID</option>
148 </conditional> 79 <option value="KEGG">Genome annotation DBs - KEGG</option>
149 <conditional name="to"> 80 <option value="PATRIC">Genome annotation DBs - PATRIC</option>
150 <expand macro="macro-category_TO"/> 81 <option value="UCSC">Genome annotation DBs - UCSC</option>
151 <when value="uniprot"> 82 <option value="WBParaSite">Genome annotation DBs - WBParaSite</option>
152 <expand macro="macro-db_uniprot_TO"/> 83 <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option>
153 </when> 84 <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option>
154 <when value="oseqdb"> 85 <option value="Araport">Organism-specific DBs - Araport</option>
155 <expand macro="macro-db_oseqdb"/> 86 <option value="CGD">Organism-specific DBs - CGD</option>
156 </when> 87 <option value="ConoServer">Organism-specific DBs - ConoServer</option>
157 <when value="3Dstrdb"> 88 <option value="dictyBase">Organism-specific DBs - dictyBase</option>
158 <expand macro="macro-db_3Dstrdb"/> 89 <option value="EchoBASE">Organism-specific DBs - EchoBASE</option>
159 </when> 90 <option value="euHCVdb">Organism-specific DBs - euHCVdb</option>
160 <when value="ppidb"> 91 <option value="FlyBase">Organism-specific DBs - FlyBase</option>
161 <expand macro="macro-db_ppidb"/> 92 <option value="GeneCards">Organism-specific DBs - GeneCards</option>
162 </when> 93 <option value="GeneReviews">Organism-specific DBs - GeneReviews</option>
163 <when value="chemistry"> 94 <option value="HGNC">Organism-specific DBs - HGNC</option>
164 <expand macro="macro-db_chemistry"/> 95 <option value="LegioList">Organism-specific DBs - LegioList</option>
165 </when> 96 <option value="Leproma">Organism-specific DBs - Leproma</option>
166 <when value="protfgdb"> 97 <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option>
167 <expand macro="macro-db_protfgdb"/> 98 <option value="MGI">Organism-specific DBs - MGI</option>
168 </when> 99 <option value="MIM">Organism-specific DBs - MIM</option>
169 <when value="polymorphismANDmutation"> 100 <option value="neXtProt">Organism-specific DBs - neXtProt</option>
170 <expand macro="macro-db_polymorphismANDmutation"/> 101 <option value="OpenTargets">Organism-specific DBs - OpenTargets</option>
171 </when> 102 <option value="Orphanet">Organism-specific DBs - Orphanet</option>
172 <when value="2DgelDB"> 103 <option value="PharmGKB">Organism-specific DBs - PharmGKB</option>
173 <expand macro="macro-db_2DgelDB"/> 104 <option value="PomBase">Organism-specific DBs - PomBase</option>
174 </when> 105 <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option>
175 <when value="ProtocolsMaterialsDB"> 106 <option value="RGD">Organism-specific DBs - RGD</option>
176 <expand macro="macro-db_ProtocolsMaterialsDB"/> 107 <option value="SGD">Organism-specific DBs - SGD</option>
177 </when> 108 <option value="TubercuList">Organism-specific DBs - TubercuList</option>
178 <when value="GenomeAnnotationDB"> 109 <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option>
179 <expand macro="macro-db_GenomeAnnotationDB"/> 110 <option value="VGNC">Organism-specific DBs - VGNC</option>
180 </when> 111 <option value="WormBase">Organism-specific DBs - WormBase</option>
181 <when value="OrganismSpecificGeneDB"> 112 <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option>
182 <expand macro="macro-db_OrganismSpecificGeneDB"/> 113 <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option>
183 </when> 114 <option value="Xenbase">Organism-specific DBs - Xenbase</option>
184 <when value="phylogenomic"> 115 <option value="ZFIN">Organism-specific DBs - ZFIN</option>
185 <expand macro="macro-db_phylogenomic"/> 116 <option value="eggNOG">Phylogenomic DBs - eggNOG</option>
186 </when> 117 <option value="GeneTree">Phylogenomic DBs - GeneTree</option>
187 <when value="EnzymePathwayDB"> 118 <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option>
188 <expand macro="macro-db_EnzymePathwayDB"/> 119 <option value="OMA">Phylogenomic DBs - OMA</option>
189 </when> 120 <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option>
190 <when value="GeneExpression"> 121 <option value="TreeFam">Phylogenomic DBs - TreeFam</option>
191 <expand macro="macro-db_GeneExpression"/> 122 <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option>
192 </when> 123 <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option>
193 <when value="other"> 124 <option value="Reactome">Enzyme and pathway DBs - Reactome</option>
194 <expand macro="macro-db_other"/> 125 <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option>
126 <option value="ChiTaRS">Miscellaneous - ChiTaRS</option>
127 <option value="GeneWiki">Miscellaneous - GeneWiki</option>
128 <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option>
129 <option value="PHI-base">Miscellaneous - PHI-base</option>
130 <option value="CollecTF">Gene expression DBs - CollecTF</option>
131 <option value="DisProt">Family and domain DBs - DisProt</option>
132 <option value="IDEAL">Family and domain DBs - IDEAL</option>
133 </param>
134 <when value="UniProtKB_AC-ID">
135 <param name="to" type="select" label="Target database:">
136 <option value="CCDS">Sequence DBs - CCDS</option>
137 <option value="PIR">Sequence DBs - PIR</option>
138 <option value="PDB">3D structure DBs - PDB</option>
139 <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option>
140 <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option>
141 <option value="DIP">Protein-protein interaction DBs - DIP</option>
142 <option value="STRING">Protein-protein interaction DBs - STRING</option>
143 <option value="ChEMBL">Chemistry - ChEMBL</option>
144 <option value="DrugBank">Chemistry - DrugBank</option>
145 <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option>
146 <option value="SwissLipids">Chemistry - SwissLipids</option>
147 <option value="Allergome">Protein family/group DBs - Allergome</option>
148 <option value="ESTHER">Protein family/group DBs - ESTHER</option>
149 <option value="MEROPS">Protein family/group DBs - MEROPS</option>
150 <option value="CLAE">Protein family/group DBs - CLAE</option>
151 <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option>
152 <option value="REBASE">Protein family/group DBs - REBASE</option>
153 <option value="TCDB">Protein family/group DBs - TCDB</option>
154 <option value="GlyConnect">PTM DBs - GlyConnect</option>
155 <option value="BioMuta">Genetic variation DBs - BioMuta</option>
156 <option value="DMDM">Genetic variation DBs - DMDM</option>
157 <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option>
158 <option value="CPTAC">Proteomic DBs - CPTAC</option>
159 <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option>
160 <option value="DNASU">Protocols and materials DBs - DNASU</option>
161 <option value="Ensembl">Genome annotation DBs - Ensembl</option>
162 <option value="GeneID">Genome annotation DBs - GeneID</option>
163 <option value="KEGG">Genome annotation DBs - KEGG</option>
164 <option value="PATRIC">Genome annotation DBs - PATRIC</option>
165 <option value="UCSC">Genome annotation DBs - UCSC</option>
166 <option value="WBParaSite">Genome annotation DBs - WBParaSite</option>
167 <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option>
168 <option value="Araport">Organism-specific DBs - Araport</option>
169 <option value="CGD">Organism-specific DBs - CGD</option>
170 <option value="ConoServer">Organism-specific DBs - ConoServer</option>
171 <option value="dictyBase">Organism-specific DBs - dictyBase</option>
172 <option value="EchoBASE">Organism-specific DBs - EchoBASE</option>
173 <option value="euHCVdb">Organism-specific DBs - euHCVdb</option>
174 <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option>
175 <option value="FlyBase">Organism-specific DBs - FlyBase</option>
176 <option value="GeneCards">Organism-specific DBs - GeneCards</option>
177 <option value="GeneReviews">Organism-specific DBs - GeneReviews</option>
178 <option value="HGNC">Organism-specific DBs - HGNC</option>
179 <option value="LegioList">Organism-specific DBs - LegioList</option>
180 <option value="Leproma">Organism-specific DBs - Leproma</option>
181 <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option>
182 <option value="MGI">Organism-specific DBs - MGI</option>
183 <option value="MIM">Organism-specific DBs - MIM</option>
184 <option value="neXtProt">Organism-specific DBs - neXtProt</option>
185 <option value="OpenTargets">Organism-specific DBs - OpenTargets</option>
186 <option value="Orphanet">Organism-specific DBs - Orphanet</option>
187 <option value="PharmGKB">Organism-specific DBs - PharmGKB</option>
188 <option value="PomBase">Organism-specific DBs - PomBase</option>
189 <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option>
190 <option value="RGD">Organism-specific DBs - RGD</option>
191 <option value="SGD">Organism-specific DBs - SGD</option>
192 <option value="TubercuList">Organism-specific DBs - TubercuList</option>
193 <option value="VGNC">Organism-specific DBs - VGNC</option>
194 <option value="WormBase">Organism-specific DBs - WormBase</option>
195 <option value="Xenbase">Organism-specific DBs - Xenbase</option>
196 <option value="ZFIN">Organism-specific DBs - ZFIN</option>
197 <option value="eggNOG">Phylogenomic DBs - eggNOG</option>
198 <option value="GeneTree">Phylogenomic DBs - GeneTree</option>
199 <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option>
200 <option value="OMA">Phylogenomic DBs - OMA</option>
201 <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option>
202 <option value="TreeFam">Phylogenomic DBs - TreeFam</option>
203 <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option>
204 <option value="Reactome">Enzyme and pathway DBs - Reactome</option>
205 <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option>
206 <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option>
207 <option value="ChiTaRS">Miscellaneous - ChiTaRS</option>
208 <option value="GeneWiki">Miscellaneous - GeneWiki</option>
209 <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option>
210 <option value="PHI-base">Miscellaneous - PHI-base</option>
211 <option value="CollecTF">Gene expression DBs - CollecTF</option>
212 <option value="IDEAL">Family and domain DBs - IDEAL</option>
213 <option value="DisProt">Family and domain DBs - DisProt</option>
214 <option value="UniProtKB">UniProt - UniProtKB</option>
215 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
216 <option value="UniParc">UniProt - UniParc</option>
217 <option value="UniRef50">UniProt - UniRef50</option>
218 <option value="UniRef90">UniProt - UniRef90</option>
219 <option value="UniRef100">UniProt - UniRef100</option>
220 <option value="Gene_Name">UniProt - Gene Name</option>
221 <option value="CRC64">UniProt - CRC64</option>
222 <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option>
223 <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option>
224 <option value="GI_number">Sequence DBs - GI number</option>
225 <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option>
226 <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option>
227 <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option>
228 <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option>
229 <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option>
230 <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option>
231 <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option>
232 <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option>
233 <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option>
234 <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option>
235 </param>
236 </when>
237 <when value="UniParc">
238 <param name="to" type="select" label="Target database:">
239 <option value="UniProtKB">UniProt - UniProtKB</option>
240 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
241 <option value="UniParc">UniProt - UniParc</option>
242 </param>
243 </when>
244 <when value="UniRef50">
245 <param name="to" type="select" label="Target database:">
246 <option value="UniProtKB">UniProt - UniProtKB</option>
247 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
248 <option value="UniRef50">UniProt - UniRef50</option>
249 </param>
250 </when>
251 <when value="UniRef90">
252 <param name="to" type="select" label="Target database:">
253 <option value="UniProtKB">UniProt - UniProtKB</option>
254 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
255 <option value="UniRef90">UniProt - UniRef90</option>
256 </param>
257 </when>
258 <when value="UniRef100">
259 <param name="to" type="select" label="Target database:">
260 <option value="UniProtKB">UniProt - UniProtKB</option>
261 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
262 <option value="UniRef100">UniProt - UniRef100</option>
263 </param>
264 </when>
265 <when value="Gene_Name">
266 <param name="to" type="select" label="Target database:">
267 <option value="UniProtKB">UniProt - UniProtKB</option>
268 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
269 </param>
270 </when>
271 <when value="CRC64">
272 <param name="to" type="select" label="Target database:">
273 <option value="UniProtKB">UniProt - UniProtKB</option>
274 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
275 </param>
276 </when>
277 <when value="CCDS">
278 <param name="to" type="select" label="Target database:">
279 <option value="UniProtKB">UniProt - UniProtKB</option>
280 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
281 </param>
282 </when>
283 <when value="EMBL-GenBank-DDBJ">
284 <param name="to" type="select" label="Target database:">
285 <option value="UniProtKB">UniProt - UniProtKB</option>
286 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
287 </param>
288 </when>
289 <when value="EMBL-GenBank-DDBJ_CDS">
290 <param name="to" type="select" label="Target database:">
291 <option value="UniProtKB">UniProt - UniProtKB</option>
292 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
293 </param>
294 </when>
295 <when value="GI_number">
296 <param name="to" type="select" label="Target database:">
297 <option value="UniProtKB">UniProt - UniProtKB</option>
298 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
299 </param>
300 </when>
301 <when value="PIR">
302 <param name="to" type="select" label="Target database:">
303 <option value="UniProtKB">UniProt - UniProtKB</option>
304 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
305 </param>
306 </when>
307 <when value="RefSeq_Nucleotide">
308 <param name="to" type="select" label="Target database:">
309 <option value="UniProtKB">UniProt - UniProtKB</option>
310 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
311 </param>
312 </when>
313 <when value="RefSeq_Protein">
314 <param name="to" type="select" label="Target database:">
315 <option value="UniProtKB">UniProt - UniProtKB</option>
316 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
317 </param>
318 </when>
319 <when value="PDB">
320 <param name="to" type="select" label="Target database:">
321 <option value="UniProtKB">UniProt - UniProtKB</option>
322 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
323 </param>
324 </when>
325 <when value="BioGRID">
326 <param name="to" type="select" label="Target database:">
327 <option value="UniProtKB">UniProt - UniProtKB</option>
328 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
329 </param>
330 </when>
331 <when value="ComplexPortal">
332 <param name="to" type="select" label="Target database:">
333 <option value="UniProtKB">UniProt - UniProtKB</option>
334 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
335 </param>
336 </when>
337 <when value="DIP">
338 <param name="to" type="select" label="Target database:">
339 <option value="UniProtKB">UniProt - UniProtKB</option>
340 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
341 </param>
342 </when>
343 <when value="STRING">
344 <param name="to" type="select" label="Target database:">
345 <option value="UniProtKB">UniProt - UniProtKB</option>
346 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
347 </param>
348 </when>
349 <when value="ChEMBL">
350 <param name="to" type="select" label="Target database:">
351 <option value="UniProtKB">UniProt - UniProtKB</option>
352 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
353 </param>
354 </when>
355 <when value="DrugBank">
356 <param name="to" type="select" label="Target database:">
357 <option value="UniProtKB">UniProt - UniProtKB</option>
358 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
359 </param>
360 </when>
361 <when value="GuidetoPHARMACOLOGY">
362 <param name="to" type="select" label="Target database:">
363 <option value="UniProtKB">UniProt - UniProtKB</option>
364 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
365 </param>
366 </when>
367 <when value="SwissLipids">
368 <param name="to" type="select" label="Target database:">
369 <option value="UniProtKB">UniProt - UniProtKB</option>
370 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
371 </param>
372 </when>
373 <when value="Allergome">
374 <param name="to" type="select" label="Target database:">
375 <option value="UniProtKB">UniProt - UniProtKB</option>
376 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
377 </param>
378 </when>
379 <when value="CLAE">
380 <param name="to" type="select" label="Target database:">
381 <option value="UniProtKB">UniProt - UniProtKB</option>
382 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
383 </param>
384 </when>
385 <when value="ESTHER">
386 <param name="to" type="select" label="Target database:">
387 <option value="UniProtKB">UniProt - UniProtKB</option>
388 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
389 </param>
390 </when>
391 <when value="MEROPS">
392 <param name="to" type="select" label="Target database:">
393 <option value="UniProtKB">UniProt - UniProtKB</option>
394 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
395 </param>
396 </when>
397 <when value="PeroxiBase">
398 <param name="to" type="select" label="Target database:">
399 <option value="UniProtKB">UniProt - UniProtKB</option>
400 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
401 </param>
402 </when>
403 <when value="REBASE">
404 <param name="to" type="select" label="Target database:">
405 <option value="UniProtKB">UniProt - UniProtKB</option>
406 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
407 </param>
408 </when>
409 <when value="TCDB">
410 <param name="to" type="select" label="Target database:">
411 <option value="UniProtKB">UniProt - UniProtKB</option>
412 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
413 </param>
414 </when>
415 <when value="GlyConnect">
416 <param name="to" type="select" label="Target database:">
417 <option value="UniProtKB">UniProt - UniProtKB</option>
418 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
419 </param>
420 </when>
421 <when value="BioMuta">
422 <param name="to" type="select" label="Target database:">
423 <option value="UniProtKB">UniProt - UniProtKB</option>
424 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
425 </param>
426 </when>
427 <when value="DMDM">
428 <param name="to" type="select" label="Target database:">
429 <option value="UniProtKB">UniProt - UniProtKB</option>
430 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
431 </param>
432 </when>
433 <when value="World-2DPAGE">
434 <param name="to" type="select" label="Target database:">
435 <option value="UniProtKB">UniProt - UniProtKB</option>
436 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
437 </param>
438 </when>
439 <when value="CPTAC">
440 <param name="to" type="select" label="Target database:">
441 <option value="UniProtKB">UniProt - UniProtKB</option>
442 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
443 </param>
444 </when>
445 <when value="ProteomicsDB">
446 <param name="to" type="select" label="Target database:">
447 <option value="UniProtKB">UniProt - UniProtKB</option>
448 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
449 </param>
450 </when>
451 <when value="DNASU">
452 <param name="to" type="select" label="Target database:">
453 <option value="UniProtKB">UniProt - UniProtKB</option>
454 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
455 </param>
456 </when>
457 <when value="Ensembl">
458 <param name="to" type="select" label="Target database:">
459 <option value="UniProtKB">UniProt - UniProtKB</option>
460 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
461 </param>
462 </when>
463 <when value="Ensembl_Genomes">
464 <param name="to" type="select" label="Target database:">
465 <option value="UniProtKB">UniProt - UniProtKB</option>
466 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
467 </param>
468 </when>
469 <when value="Ensembl_Genomes_Protein">
470 <param name="to" type="select" label="Target database:">
471 <option value="UniProtKB">UniProt - UniProtKB</option>
472 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
473 </param>
474 </when>
475 <when value="Ensembl_Genomes_Transcript">
476 <param name="to" type="select" label="Target database:">
477 <option value="UniProtKB">UniProt - UniProtKB</option>
478 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
479 </param>
480 </when>
481 <when value="Ensembl_Protein">
482 <param name="to" type="select" label="Target database:">
483 <option value="UniProtKB">UniProt - UniProtKB</option>
484 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
485 </param>
486 </when>
487 <when value="Ensembl_Transcript">
488 <param name="to" type="select" label="Target database:">
489 <option value="UniProtKB">UniProt - UniProtKB</option>
490 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
491 </param>
492 </when>
493 <when value="GeneID">
494 <param name="to" type="select" label="Target database:">
495 <option value="UniProtKB">UniProt - UniProtKB</option>
496 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
497 </param>
498 </when>
499 <when value="KEGG">
500 <param name="to" type="select" label="Target database:">
501 <option value="UniProtKB">UniProt - UniProtKB</option>
502 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
503 </param>
504 </when>
505 <when value="PATRIC">
506 <param name="to" type="select" label="Target database:">
507 <option value="UniProtKB">UniProt - UniProtKB</option>
508 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
509 </param>
510 </when>
511 <when value="UCSC">
512 <param name="to" type="select" label="Target database:">
513 <option value="UniProtKB">UniProt - UniProtKB</option>
514 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
515 </param>
516 </when>
517 <when value="WBParaSite">
518 <param name="to" type="select" label="Target database:">
519 <option value="UniProtKB">UniProt - UniProtKB</option>
520 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
521 </param>
522 </when>
523 <when value="WBParaSite_Transcript-Protein">
524 <param name="to" type="select" label="Target database:">
525 <option value="UniProtKB">UniProt - UniProtKB</option>
526 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
527 </param>
528 </when>
529 <when value="ArachnoServer">
530 <param name="to" type="select" label="Target database:">
531 <option value="UniProtKB">UniProt - UniProtKB</option>
532 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
533 </param>
534 </when>
535 <when value="Araport">
536 <param name="to" type="select" label="Target database:">
537 <option value="UniProtKB">UniProt - UniProtKB</option>
538 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
539 </param>
540 </when>
541 <when value="CGD">
542 <param name="to" type="select" label="Target database:">
543 <option value="UniProtKB">UniProt - UniProtKB</option>
544 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
545 </param>
546 </when>
547 <when value="ConoServer">
548 <param name="to" type="select" label="Target database:">
549 <option value="UniProtKB">UniProt - UniProtKB</option>
550 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
551 </param>
552 </when>
553 <when value="dictyBase">
554 <param name="to" type="select" label="Target database:">
555 <option value="UniProtKB">UniProt - UniProtKB</option>
556 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
557 </param>
558 </when>
559 <when value="EchoBASE">
560 <param name="to" type="select" label="Target database:">
561 <option value="UniProtKB">UniProt - UniProtKB</option>
562 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
563 </param>
564 </when>
565 <when value="euHCVdb">
566 <param name="to" type="select" label="Target database:">
567 <option value="UniProtKB">UniProt - UniProtKB</option>
568 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
569 </param>
570 </when>
571 <when value="FlyBase">
572 <param name="to" type="select" label="Target database:">
573 <option value="UniProtKB">UniProt - UniProtKB</option>
574 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
575 </param>
576 </when>
577 <when value="GeneCards">
578 <param name="to" type="select" label="Target database:">
579 <option value="UniProtKB">UniProt - UniProtKB</option>
580 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
581 </param>
582 </when>
583 <when value="GeneReviews">
584 <param name="to" type="select" label="Target database:">
585 <option value="UniProtKB">UniProt - UniProtKB</option>
586 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
587 </param>
588 </when>
589 <when value="HGNC">
590 <param name="to" type="select" label="Target database:">
591 <option value="UniProtKB">UniProt - UniProtKB</option>
592 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
593 </param>
594 </when>
595 <when value="LegioList">
596 <param name="to" type="select" label="Target database:">
597 <option value="UniProtKB">UniProt - UniProtKB</option>
598 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
599 </param>
600 </when>
601 <when value="Leproma">
602 <param name="to" type="select" label="Target database:">
603 <option value="UniProtKB">UniProt - UniProtKB</option>
604 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
605 </param>
606 </when>
607 <when value="MaizeGDB">
608 <param name="to" type="select" label="Target database:">
609 <option value="UniProtKB">UniProt - UniProtKB</option>
610 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
611 </param>
612 </when>
613 <when value="MGI">
614 <param name="to" type="select" label="Target database:">
615 <option value="UniProtKB">UniProt - UniProtKB</option>
616 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
617 </param>
618 </when>
619 <when value="MIM">
620 <param name="to" type="select" label="Target database:">
621 <option value="UniProtKB">UniProt - UniProtKB</option>
622 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
623 </param>
624 </when>
625 <when value="neXtProt">
626 <param name="to" type="select" label="Target database:">
627 <option value="UniProtKB">UniProt - UniProtKB</option>
628 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
629 </param>
630 </when>
631 <when value="OpenTargets">
632 <param name="to" type="select" label="Target database:">
633 <option value="UniProtKB">UniProt - UniProtKB</option>
634 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
635 </param>
636 </when>
637 <when value="Orphanet">
638 <param name="to" type="select" label="Target database:">
639 <option value="UniProtKB">UniProt - UniProtKB</option>
640 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
641 </param>
642 </when>
643 <when value="PharmGKB">
644 <param name="to" type="select" label="Target database:">
645 <option value="UniProtKB">UniProt - UniProtKB</option>
646 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
647 </param>
648 </when>
649 <when value="PomBase">
650 <param name="to" type="select" label="Target database:">
651 <option value="UniProtKB">UniProt - UniProtKB</option>
652 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
653 </param>
654 </when>
655 <when value="PseudoCAP">
656 <param name="to" type="select" label="Target database:">
657 <option value="UniProtKB">UniProt - UniProtKB</option>
658 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
659 </param>
660 </when>
661 <when value="RGD">
662 <param name="to" type="select" label="Target database:">
663 <option value="UniProtKB">UniProt - UniProtKB</option>
664 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
665 </param>
666 </when>
667 <when value="SGD">
668 <param name="to" type="select" label="Target database:">
669 <option value="UniProtKB">UniProt - UniProtKB</option>
670 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
671 </param>
672 </when>
673 <when value="TubercuList">
674 <param name="to" type="select" label="Target database:">
675 <option value="UniProtKB">UniProt - UniProtKB</option>
676 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
677 </param>
678 </when>
679 <when value="VEuPathDB">
680 <param name="to" type="select" label="Target database:">
681 <option value="UniProtKB">UniProt - UniProtKB</option>
682 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
683 </param>
684 </when>
685 <when value="VGNC">
686 <param name="to" type="select" label="Target database:">
687 <option value="UniProtKB">UniProt - UniProtKB</option>
688 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
689 </param>
690 </when>
691 <when value="WormBase">
692 <param name="to" type="select" label="Target database:">
693 <option value="UniProtKB">UniProt - UniProtKB</option>
694 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
695 </param>
696 </when>
697 <when value="WormBase_Protein">
698 <param name="to" type="select" label="Target database:">
699 <option value="UniProtKB">UniProt - UniProtKB</option>
700 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
701 </param>
702 </when>
703 <when value="WormBase_Transcript">
704 <param name="to" type="select" label="Target database:">
705 <option value="UniProtKB">UniProt - UniProtKB</option>
706 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
707 </param>
708 </when>
709 <when value="Xenbase">
710 <param name="to" type="select" label="Target database:">
711 <option value="UniProtKB">UniProt - UniProtKB</option>
712 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
713 </param>
714 </when>
715 <when value="ZFIN">
716 <param name="to" type="select" label="Target database:">
717 <option value="UniProtKB">UniProt - UniProtKB</option>
718 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
719 </param>
720 </when>
721 <when value="eggNOG">
722 <param name="to" type="select" label="Target database:">
723 <option value="UniProtKB">UniProt - UniProtKB</option>
724 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
725 </param>
726 </when>
727 <when value="GeneTree">
728 <param name="to" type="select" label="Target database:">
729 <option value="UniProtKB">UniProt - UniProtKB</option>
730 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
731 </param>
732 </when>
733 <when value="HOGENOM">
734 <param name="to" type="select" label="Target database:">
735 <option value="UniProtKB">UniProt - UniProtKB</option>
736 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
737 </param>
738 </when>
739 <when value="OMA">
740 <param name="to" type="select" label="Target database:">
741 <option value="UniProtKB">UniProt - UniProtKB</option>
742 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
743 </param>
744 </when>
745 <when value="OrthoDB">
746 <param name="to" type="select" label="Target database:">
747 <option value="UniProtKB">UniProt - UniProtKB</option>
748 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
749 </param>
750 </when>
751 <when value="TreeFam">
752 <param name="to" type="select" label="Target database:">
753 <option value="UniProtKB">UniProt - UniProtKB</option>
754 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
755 </param>
756 </when>
757 <when value="BioCyc">
758 <param name="to" type="select" label="Target database:">
759 <option value="UniProtKB">UniProt - UniProtKB</option>
760 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
761 </param>
762 </when>
763 <when value="PlantReactome">
764 <param name="to" type="select" label="Target database:">
765 <option value="UniProtKB">UniProt - UniProtKB</option>
766 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
767 </param>
768 </when>
769 <when value="Reactome">
770 <param name="to" type="select" label="Target database:">
771 <option value="UniProtKB">UniProt - UniProtKB</option>
772 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
773 </param>
774 </when>
775 <when value="UniPathway">
776 <param name="to" type="select" label="Target database:">
777 <option value="UniProtKB">UniProt - UniProtKB</option>
778 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
779 </param>
780 </when>
781 <when value="ChiTaRS">
782 <param name="to" type="select" label="Target database:">
783 <option value="UniProtKB">UniProt - UniProtKB</option>
784 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
785 </param>
786 </when>
787 <when value="GeneWiki">
788 <param name="to" type="select" label="Target database:">
789 <option value="UniProtKB">UniProt - UniProtKB</option>
790 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
791 </param>
792 </when>
793 <when value="GenomeRNAi">
794 <param name="to" type="select" label="Target database:">
795 <option value="UniProtKB">UniProt - UniProtKB</option>
796 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
797 </param>
798 </when>
799 <when value="PHI-base">
800 <param name="to" type="select" label="Target database:">
801 <option value="UniProtKB">UniProt - UniProtKB</option>
802 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
803 </param>
804 </when>
805 <when value="CollecTF">
806 <param name="to" type="select" label="Target database:">
807 <option value="UniProtKB">UniProt - UniProtKB</option>
808 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
809 </param>
810 </when>
811 <when value="DisProt">
812 <param name="to" type="select" label="Target database:">
813 <option value="UniProtKB">UniProt - UniProtKB</option>
814 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
815 </param>
816 </when>
817 <when value="IDEAL">
818 <param name="to" type="select" label="Target database:">
819 <option value="UniProtKB">UniProt - UniProtKB</option>
820 <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option>
821 </param>
195 </when> 822 </when>
196 </conditional> 823 </conditional>
197 </when> 824 </when>
198 <when value="retrieve"> 825 <when value="retrieve">
199 <param name="format" type="select" label="Choose format of output file" help=""> 826 <param name="format" type="select" label="Choose format of output file" help="">
204 </when> 831 </when>
205 </conditional> 832 </conditional>
206 </inputs> 833 </inputs>
207 <outputs> 834 <outputs>
208 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" 835 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
209 label="${tool.name} on ${on_string} (retrieve output)"> 836 label="${tool.name} on ${on_string}: fasta">
210 <filter>tool['tool_choice'] == 'retrieve'</filter> 837 <filter>tool['tool_choice'] == 'retrieve'</filter>
211 <filter>tool['format'] == 'fasta'</filter> 838 <filter>tool['format'] == 'fasta'</filter>
212 </data> 839 </data>
213 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output" 840 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
214 label="${tool.name} on ${on_string} (retrieve output)"> 841 label="${tool.name} on ${on_string}: gff">
215 <filter>tool['tool_choice'] == 'retrieve'</filter> 842 <filter>tool['tool_choice'] == 'retrieve'</filter>
216 <filter>tool['format'] == 'gff'</filter> 843 <filter>tool['format'] == 'gff'</filter>
217 </data> 844 </data>
218 <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output" 845 <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
219 label="${tool.name} on ${on_string} (retrieve output)"> 846 label="${tool.name} on ${on_string}: txt">
220 <filter>tool['tool_choice'] == 'retrieve'</filter> 847 <filter>tool['tool_choice'] == 'retrieve'</filter>
221 <filter>tool['format'] == 'txt'</filter> 848 <filter>tool['format'] == 'txt'</filter>
222 </data> 849 </data>
223 <data name="outfile_map" format="tabular" from_work_dir="./output" 850 <data name="outfile_map" format="tabular" from_work_dir="./output"
224 label="${tool.name} on ${on_string} (map output)"> 851 label="${tool.name} on ${on_string}: mapping">
225 <filter>tool['tool_choice'] == 'map'</filter> 852 <filter>tool['tool_choice'] == 'map'</filter>
226 </data> 853 </data>
227 </outputs> 854 </outputs>
228 <tests> 855 <tests>
229 <test> 856 <test expect_num_outputs="1">
230 <param name="infile" value="id_uniprot.tab" ftype="tabular"/> 857 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
231 <param name="id_column" value="c1"/> 858 <param name="id_column" value="c1"/>
232 <param name="format" value="fasta"/> 859 <param name="format" value="fasta"/>
233 <param name="tool_choice" value="retrieve"/> 860 <param name="tool_choice" value="retrieve"/>
234 <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" /> 861 <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" />
235 </test> 862 </test>
236 <test> 863 <test expect_num_outputs="1">
237 <param name="infile" value="id_uniprot.tab" ftype="tabular"/> 864 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
238 <param name="id_column" value="c1"/> 865 <param name="id_column" value="c1"/>
239 <param name="format" value="gff"/> 866 <param name="format" value="gff"/>
240 <param name="tool_choice" value="retrieve"/> 867 <param name="tool_choice" value="retrieve"/>
241 <output name="outfile_retrieve_gff" file="test2_retrieve.gff" ftype="gff" compare="sim_size" /> 868 <output name="outfile_retrieve_gff" file="test2_retrieve.gff" ftype="gff" compare="sim_size" />
242 </test> 869 </test>
243 <test> 870 <test expect_num_outputs="1">
244 <param name="infile" value="id_uniprot.tab" ftype="tabular"/> 871 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
245 <param name="id_column" value="c1"/> 872 <param name="id_column" value="c1"/>
246 <param name="tool_choice" value="map"/> 873 <param name="tool_choice" value="map"/>
247 <param name="category_FROM" value="uniprot"/> 874 <param name="from" value="UniProtKB_AC-ID"/>
248 <param name="db_uniprot_FROM" value="ID"/> 875 <param name="to" value="Gene_Name"/>
249 <param name="category_TO" value="uniprot"/>
250 <param name="db_uniprot_TO" value="GENENAME"/>
251 <output name="outfile_map" file="test1_map.tab" ftype="tabular"/> 876 <output name="outfile_map" file="test1_map.tab" ftype="tabular"/>
252 </test> 877 </test>
253 <test> 878 <test expect_num_outputs="1">
254 <param name="infile" value="id_map_refseq.txt" ftype="tabular"/> 879 <param name="infile" value="id_map_refseq.txt" ftype="tabular"/>
255 <param name="id_column" value="c1"/> 880 <param name="id_column" value="c1"/>
256 <param name="tool_choice" value="map"/> 881 <param name="tool_choice" value="map"/>
257 <param name="category_FROM" value="oseqdb"/> 882 <param name="from" value="RefSeq_Nucleotide"/>
258 <param name="db_oseqdb" value="REFSEQ_NT_ID"/> 883 <param name="to" value="UniProtKB"/>
259 <param name="category_TO" value="uniprot"/>
260 <param name="db_uniprot_TO" value="ID"/>
261 <output name="outfile_map" file="test2_map.tab" ftype="tabular"/> 884 <output name="outfile_map" file="test2_map.tab" ftype="tabular"/>
262 </test> 885 </test>
263 </tests> 886 </tests>
264 <help><![CDATA[ 887 <help><![CDATA[
265 888