Mercurial > repos > bgruening > uniprot_rest_interface

comparison macros.xml @ 0:48522382b6a4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
author bgruening
date Fri, 09 Oct 2015 16:42:22 -0400
parents
children bfdc6a7ffd3a
comparison
equal deleted inserted replaced
-1:000000000000 0:48522382b6a4
1 <macros>
2 <token name="@EXECUTABLE@">1.0</token>
3 <macro name="macro-category_FROM">
4 <param name="category_FROM" type="select" label="Choose your database category (FROM):"
5 help="Select a databse from which your ids are coming from">
6 <option value="uniprot">UniProt</option>
7 <option value="oseqdb">Other sequence databases</option>
8 <option value="3Dstrdb">3D structure databases</option>
9 <option value="ppidb">Protein-protein interaction databases</option>
10 <option value="chemistry">Chemistry</option>
11 <option value="protfgdb">Protein family/group databases</option>
12 <option value="polymorphismANDmutation">Polymorphism and mutation databases</option>
13 <option value="2DgelDB">2D gel databases</option>
14 <option value="ProtocolsMaterialsDB">Protocols and materials databases</option>
15 <option value="GenomeAnnotationDB">Genome annotation databases</option>
16 <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option>
17 <option value="phylogenomic">Phylogenomic databases</option>
18 <option value="EnzymePathwayDB">Enzyme and pathway databases</option>
19 <option value="GeneExpression">Gene expression databases</option>
20 <option value="other">Other</option>
21 </param>
22 </macro>
23 <macro name="macro-category_TO">
24 <param name="category_TO" type="select" label="Choose your database category (TO):"
25 help="Select a database which will be used for mapping">
26 <option value="uniprot">UniProt</option>
27 <option value="oseqdb">Other sequence databases</option>
28 <option value="3Dstrdb">3D structure databases</option>
29 <option value="ppidb">Protein-protein interaction databases</option>
30 <option value="chemistry">Chemistry</option>
31 <option value="protfgdb">Protein family/group databases</option>
32 <option value="polymorphismANDmutation">Polymorphism and mutation databases</option>
33 <option value="2DgelDB">2D gel databases</option>
34 <option value="ProtocolsMaterialsDB">Protocols and materials databases</option>
35 <option value="GenomeAnnotationDB">Genome annotation databases</option>
36 <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option>
37 <option value="phylogenomic">Phylogenomic databases</option>
38 <option value="EnzymePathwayDB">Enzyme and pathway databases</option>
39 <option value="GeneExpression">Gene expression databases</option>
40 <option value="other">Other</option>
41 </param>
42 </macro>
43 <macro name="macro-db_uniprot_FROM">
44 <param name="db_uniprot_FROM" type="select" label="Choose a database:"
45 help="">
46 <option value="ACC+ID">UniProtKB AC/ID</option>
47 <option value="ACC">UniProtKB AC</option>
48 <option value="ID">UniProtKB ID</option>
49 <option value="ACC">UniProtKB AC</option>
50 <option value="UPARC">UniParc</option>
51 <option value="NF50">UniRef50</option>
52 <option value="NF90">UniRef90</option>
53 <option value="NF100">UniRef100</option>
54 <option value="GENENAME">Gene name</option>
55 </param>
56 </macro>
57 <macro name="macro-db_uniprot_TO">
58 <param name="db_uniprot_TO" type="select" label="Choose a database:"
59 help="">
60 <option value="ACC">UniProtKB AC</option>
61 <option value="ID">UniProtKB ID</option>
62 <option value="ACC">UniProtKB AC</option>
63 <option value="UPARC">UniParc</option>
64 <option value="NF50">UniRef50</option>
65 <option value="NF90">UniRef90</option>
66 <option value="NF100">UniRef100</option>
67 <option value="GENENAME">Gene name</option>
68 </param>
69 </macro>
70 <macro name="macro-db_oseqdb">
71 <param name="db_oseqdb" type="select" label="Choose a database:"
72 help="">
73 <option value="EMBL_ID">EMBL/GenBank/DDBJ</option>
74 <option value="EMBL">EMBL/GenBank/DDBJ CDS</option>
75 <option value="PIR">PIR</option>
76
77 <option value="UNIGENE_ID">UniParc</option>
78 <option value="P_ENTREZGENEID">Entrez Gene (GeneID)</option>
79 <option value="P_GI">GI number</option>
80 <option value="P_REFSEQ_AC">RefSeq Protein</option>
81 <option value="REFSEQ_NT_ID">RefSeq Nucleotide</option>
82 </param>
83 </macro>
84 <macro name="macro-db_3Dstrdb">
85 <param name="db_3Dstrdb" type="select" label="Choose a database:"
86 help="">
87 <option value="PDB_ID">PDB</option>
88 <option value="DISPROT_ID">DisProt</option>
89 </param>
90 </macro>
91 <macro name="macro-db_ppidb">
92 <param name="db_ppidb" type="select" label="Choose a database:"
93 help="">
94 <option value="BIOGRID_ID">BioGrid</option>
95 <option value="DIP_ID">DIP</option>
96 <option value="MINT_ID">MINT</option>
97 <option value="STRING_ID">STRING</option>
98 </param>
99 </macro>
100 <macro name="macro-db_chemistry">
101 <param name="db_chemistry" type="select" label="Choose a database:"
102 help="">
103 <option value="CHEMBL_ID">ChEMBL</option>
104 <option value="DrugBank_ID">DrugBank</option>
105 <option value="GUIDETOPHARMACOLOGY_ID">GuidetoPHARMACOLOGY</option>
106 </param>
107 </macro>
108 <macro name="macro-db_protfgdb">
109 <param name="db_protfgdb" type="select" label="Choose a database:"
110 help="">
111 <option value="ALLERGOME_ID">Allergome</option>
112 <option value="MEROPS_ID">MEROPS</option>
113 <option value="MYCOCLAP_ID">mycoCLAP</option>
114 <option value="PEROXIBASE_ID">PeroxiBase</option>
115 <option value="REBASE_ID">REBASE</option>
116 <option value="TCDB_ID">TCDB</option>
117 </param>
118 </macro>
119 <macro name="macro-db_polymorphismANDmutation">
120 <param name="db_polymorphismANDmutation" type="select" label="Choose a database:"
121 help="">
122 <option value="DMDM_ID">DMDM</option>
123 </param>
124 </macro>
125 <macro name="macro-db_2DgelDB">
126 <param name="db_2DgelDB" type="select" label="Choose a database:"
127 help="">
128 <option value="WORLD_2DPAGE_ID">World-2DPAGE</option>
129 </param>
130 </macro>
131 <macro name="macro-db_ProtocolsMaterialsDB">
132 <param name="db_ProtocolsMaterialsDB" type="select" label="Choose a database:"
133 help="">
134 <option value="DNASU_ID">DNASU</option>
135 </param>
136 </macro>
137 <macro name="macro-db_GenomeAnnotationDB">
138 <param name="db_GenomeAnnotationDB" type="select" label="Choose a database:"
139 help="">
140 <option value="ENSEMBL_ID">Ensembl</option>
141 <option value="ENSEMBL_PRO_ID">Ensembl Protein</option>
142 <option value="ENSEMBL_TRS_ID">Ensembl Transcript</option>
143 <option value="ENSEMBLGENOME_ID">Ensembl Genomes</option>
144 <option value="ENSEMBLGENOME_PRO_ID">Ensembl Genomes Protein</option>
145 <option value="ENSEMBLGENOME_TRS_ID">Ensembl Genomes Transcript</option>
146 <option value="P_ENTREZGENEID">GeneID</option>
147 <option value="KEGG_ID">KEGG</option>
148 <option value="PATRIC_ID">PATRIC</option>
149 <option value="UCSC_ID">UCSC</option>
150 <option value="VECTORBASE_ID">VectorBase</option>
151 </param>
152 </macro>
153 <macro name="macro-db_OrganismSpecificGeneDB">
154 <param name="db_OrganismSpecificGeneDB" type="select" label="Choose a database:"
155 help="">
156 <option value="ARACHNOSERVER_ID">ArachnoServer</option>
157 <option value="CGD">CGD</option>
158 <option value="CONOSERVER_ID">ConoServer</option>
159 <option value="DICTYBASE_ID">dictyBase</option>
160 <option value="ECHOBASE_ID">EchoBASE</option>
161 <option value="ECOGENE_ID">EcoGene</option>
162 <option value="EUHCVDB_ID">euHCVdb</option>
163 <option value="EUPATHDB_ID">EuPathDB</option>
164 <option value="FLYBASE_ID">FlyBase</option>
165 <option value="GENECARDS_ID">GeneCards</option>
166 <option value="GENEFARM_ID">GeneFarm</option>
167 <option value="GENOLIST_ID">GenoList</option>
168 <option value="H_INVDB_ID">H-InvDB</option>
169 <option value="HGNC_ID">HGNC</option>
170 <option value="HPA_ID">HPA</option>
171 <option value="LEGIOLIST_ID">LegioList</option>
172 <option value="MAIZEGDB_ID">MaizeGDB</option>
173 <option value="MIM_ID">MIM</option>
174 <option value="MGI_ID">MGI</option>
175 <option value="NEXTPROT_ID">neXtProt</option>
176 <option value="ORPHANET_ID">Orphanet</option>
177 <option value="PHARMGKB_ID">PharmGKB</option>
178 <option value="POMBASE_ID">PomBase</option>
179 <option value="PSEUDOCAP_ID">PseudoCAP</option>
180 <option value="RGD_ID">RGD</option>
181 <option value="SGD_ID">SGD</option>
182 <option value="TAIR_ID">TAIR</option>
183 <option value="TUBERCULIST_ID">TubercuList</option>
184 <option value="WORMBASE_ID">WormBase</option>
185 <option value="WORMBASE_TRS_ID">WormBase Transcript</option>
186 <option value="WORMBASE_PRO_ID">WormBase Protein</option>
187 <option value="XENBASE_ID">Xenbase</option>
188 <option value="ZFIN_ID">ZFIN</option>
189 </param>
190 </macro>
191 <macro name="macro-db_phylogenomic">
192 <param name="db_phylogenomic" type="select" label="Choose a database:"
193 help="">
194 <option value="EGGNOG_ID">eggNOG</option>
195 <option value="GENETREE_ID">GeneTree</option>
196 <option value="HOGENOM_ID">HOGENOM</option>
197 <option value="HOVERGEN_ID">HOVERGEN</option>
198 <option value="KO_ID">KO</option>
199 <option value="OMA_ID">OMA</option>
200 <option value="ORTHODB_ID">OrthoDB</option>
201 <option value="PROTCLUSTDB_ID">ProtClustDB</option>
202 <option value="TREEFAM_ID">TreeFam</option>
203 </param>
204 </macro>
205 <macro name="macro-db_EnzymePathwayDB">
206 <param name="db_EnzymePathwayDB" type="select" label="Choose a database:"
207 help="">
208 <option value="BIOCYC_ID">BioCyc</option>
209 <option value="REACTOME_ID">Reactome</option>
210 <option value="UNIPATHWAY_ID">UniPathWay</option>
211 </param>
212 </macro>
213 <macro name="macro-db_GeneExpression">
214 <param name="db_GeneExpression" type="select" label="Choose a database:"
215 help="">
216 <option value="CLEANEX_ID">CleanEx</option>
217 </param>
218 </macro>
219 <macro name="macro-db_other">
220 <param name="db_other" type="select" label="Choose a database:"
221 help="">
222 <option value="CHITARS_ID">ChiTaRS</option>
223 <option value="GENOMERNAI_ID">GenomeRNAi</option>
224 <option value="GENEWIKI_ID">GeneWiki</option>
225 <option value="NEXTBIO_ID">NextBio</option>
226 </param>
227 </macro>
228 </macros>