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comparison uniprot.xml @ 1:cd2a41c65447 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
author bgruening
date Fri, 14 Oct 2016 17:59:02 -0400
parents 48522382b6a4
children fe94765e8814
comparison
equal deleted inserted replaced
0:48522382b6a4 1:cd2a41c65447
22 #if $tool.tool_choice == "retrieve": 22 #if $tool.tool_choice == "retrieve":
23 retrieve -f $tool.format $infile ./output 23 retrieve -f $tool.format $infile ./output
24 #elif $tool.tool_choice == "map": 24 #elif $tool.tool_choice == "map":
25 map 25 map
26 26
27 #if $tool.from.category_FROM == "uniprot": 27 #if $tool.from.category_FROM == "uniprot"
28 $tool.from.db_uniprot_FROM 28 '${tool.from.db_uniprot_FROM}'
29 #elif $tool.from.category_FROM == "oseqdb": 29 #elif $tool.from.category_FROM == "oseqdb"
30 $tool.from.db_oseqdb 30 ${tool.from.db_oseqdb}
31 #elif $tool.from.category_FROM == "3Dstrdb": 31 #elif $tool.from.category_FROM == "3Dstrdb"
32 $tool.from.db_3Dstrdb 32 ${tool.from.db_3Dstrdb}
33 #elif $tool.from.category_FROM == "ppidb": 33 #elif $tool.from.category_FROM == "ppidb"
34 $tool.from.db_ppidb 34 ${tool.from.db_ppidb}
35 #elif $tool.from.category_FROM == "chemistry": 35 #elif $tool.from.category_FROM == "chemistry"
36 $tool.from.db_chemistry 36 ${tool.from.db_chemistry}
37 #elif $tool.from.category_FROM == "protfgdb": 37 #elif $tool.from.category_FROM == "protfgdb"
38 $tool.from.db_protfgdb 38 ${tool.from.db_protfgdb}
39 #elif $tool.from.category_FROM == "polymorphismANDmutation": 39 #elif $tool.from.category_FROM == "polymorphismANDmutation"
40 $tool.from.db_polymorphismANDmutation 40 ${tool.from.db_polymorphismANDmutation}
41 #elif $tool.from.category_FROM == "db_2DgelDB": 41 #elif $tool.from.category_FROM == "2DgelDB"
42 $tool.from.db_2DgelDB 42 ${tool.from.db_2DgelDB}
43 #elif $tool.from.category_FROM == "ProtocolsMaterialsDB": 43 #elif $tool.from.category_FROM == "ProtocolsMaterialsDB"
44 $tool.from.ProtocolsMaterialsDB 44 ${tool.from.db_ProtocolsMaterialsDB}
45 #elif $tool.from.category_FROM == "db_GenomeAnnotationDB": 45 #elif $tool.from.category_FROM == "GenomeAnnotationDB"
46 $tool.from.db_GenomeAnnotationDB 46 ${tool.from.db_GenomeAnnotationDB}
47 #elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB": 47 #elif $tool.from.category_FROM == "OrganismSpecificGeneDB"
48 $tool.from.db_OrganismSpecificGeneDB 48 ${tool.from.db_OrganismSpecificGeneDB}
49 #elif $tool.from.category_FROM == "db_phylogenomic": 49 #elif $tool.from.category_FROM == "phylogenomic"
50 $tool.from.db_phylogenomic 50 ${tool.from.db_phylogenomic}
51 #elif $tool.from.category_FROM == "db_EnzymePathwayDB": 51 #elif $tool.from.category_FROM == "EnzymePathwayDB"
52 $tool.from.db_EnzymePathwayDB 52 ${tool.from.db_EnzymePathwayDB}
53 #elif $tool.from.category_FROM == "db_GeneExpression": 53 #elif $tool.from.category_FROM == "GeneExpression"
54 $tool.from.db_GeneExpression 54 ${tool.from.db_GeneExpression}
55 #elif $tool.from.category_FROM == "db_other": 55 #elif $tool.from.category_FROM == "other"
56 $tool.from.db_other 56 ${tool.from.db_other}
57 #end if 57 #end if
58 58
59 #if $tool.to.category_TO == "uniprot": 59 #if $tool.to.category_TO == "uniprot"
60 $tool.to.db_uniprot_TO 60 ${tool.to.db_uniprot_TO}
61 #elif $tool.to.category_TO == "oseqdb": 61 #elif $tool.to.category_TO == "oseqdb"
62 $tool.to.db_oseqdb 62 ${tool.to.db_oseqdb}
63 #elif $tool.to.category_TO == "3Dstrdb": 63 #elif $tool.to.category_TO == "3Dstrdb"
64 $tool.to.db_3Dstrdb 64 ${tool.to.db_3Dstrdb}
65 #elif $tool.to.category_TO == "ppidb": 65 #elif $tool.to.category_TO == "ppidb"
66 $tool.to.db_ppidb 66 ${tool.to.db_ppidb}
67 #elif $tool.to.category_TO == "chemistry": 67 #elif $tool.to.category_TO == "chemistry"
68 $tool.to.db_chemistry 68 ${tool.to.db_chemistry}
69 #elif $tool.to.category_TO == "protfgdb": 69 #elif $tool.to.category_TO == "protfgdb"
70 $tool.to.db_protfgdb 70 ${tool.to.db_protfgdb}
71 #elif $tool.to.category_TO == "polymorphismANDmutation": 71 #elif $tool.to.category_TO == "polymorphismANDmutation"
72 $tool.to.db_polymorphismANDmutation 72 ${tool.to.db_polymorphismANDmutation}
73 #elif $tool.to.category_TO == "db_2DgelDB": 73 #elif $tool.to.category_TO == "2DgelDB"
74 $tool.to.db_2DgelDB 74 ${tool.to.db_2DgelDB}
75 #elif $tool.to.category_TO == "ProtocolsMaterialsDB": 75 #elif $tool.to.category_TO == "ProtocolsMaterialsDB"
76 $tool.to.ProtocolsMaterialsDB 76 ${tool.to.db_ProtocolsMaterialsDB}
77 #elif $tool.to.category_TO == "db_GenomeAnnotationDB": 77 #elif $tool.to.category_TO == "GenomeAnnotationDB"
78 $tool.to.db_GenomeAnnotationDB 78 ${tool.to.db_GenomeAnnotationDB}
79 #elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB": 79 #elif $tool.to.category_TO == "OrganismSpecificGeneDB"
80 $tool.to.db_OrganismSpecificGeneDB 80 ${tool.to.db_OrganismSpecificGeneDB}
81 #elif $tool.to.category_TO == "db_phylogenomic": 81 #elif $tool.to.category_TO == "phylogenomic"
82 $tool.to.db_phylogenomic 82 ${tool.to.db_phylogenomic}
83 #elif $tool.to.category_TO == "db_EnzymePathwayDB": 83 #elif $tool.to.category_TO == "EnzymePathwayDB"
84 $tool.to.db_EnzymePathwayDB 84 ${tool.to.db_EnzymePathwayDB}
85 #elif $tool.to.category_TO == "db_GeneExpression": 85 #elif $tool.to.category_TO == "GeneExpression"
86 $tool.to.db_GeneExpression 86 ${tool.to.db_GeneExpression}
87 #elif $tool.to.category_TO == "db_other": 87 #elif $tool.to.category_TO == "other"
88 $tool.to.db_other 88 ${tool.to.db_other}
89 #end if 89 #end if
90 90
91 id_file.tabular 91 id_file.tabular
92 ./output 92 ./output
93 #end if 93 #end if
203 </when> 203 </when>
204 <when value="retrieve"> 204 <when value="retrieve">
205 <param name="format" type="select" label="Choose format of output file" help=""> 205 <param name="format" type="select" label="Choose format of output file" help="">
206 <option value="fasta">fasta</option> 206 <option value="fasta">fasta</option>
207 <option value="gff">gff</option> 207 <option value="gff">gff</option>
208 <option value="txt">Text</option>
208 </param> 209 </param>
209 </when> 210 </when>
210 </conditional> 211 </conditional>
211
212 </inputs> 212 </inputs>
213 <outputs> 213 <outputs>
214 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" 214 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
215 label="${tool.name} on ${on_string} (retrieve output)"> 215 label="${tool.name} on ${on_string} (retrieve output)">
216 <filter>tool['tool_choice'] == 'retrieve'</filter> 216 <filter>tool['tool_choice'] == 'retrieve'</filter>
218 </data> 218 </data>
219 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output" 219 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
220 label="${tool.name} on ${on_string} (retrieve output)"> 220 label="${tool.name} on ${on_string} (retrieve output)">
221 <filter>tool['tool_choice'] == 'retrieve'</filter> 221 <filter>tool['tool_choice'] == 'retrieve'</filter>
222 <filter>tool['format'] == 'gff'</filter> 222 <filter>tool['format'] == 'gff'</filter>
223 </data>
224 <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
225 label="${tool.name} on ${on_string} (retrieve output)">
226 <filter>tool['tool_choice'] == 'retrieve'</filter>
227 <filter>tool['format'] == 'txt'</filter>
223 </data> 228 </data>
224 <data name="outfile_map" format="tabular" from_work_dir="./output" 229 <data name="outfile_map" format="tabular" from_work_dir="./output"
225 label="${tool.name} on ${on_string} (map output)"> 230 label="${tool.name} on ${on_string} (map output)">
226 <filter>tool['tool_choice'] == 'map'</filter> 231 <filter>tool['tool_choice'] == 'map'</filter>
227 </data> 232 </data>
276 281
277 **INPUT** 282 **INPUT**
278 283
279 The input is a list of IDs. 284 The input is a list of IDs.
280 285
281 *example*: 286 *Example*::
282 287
283 Q0P8A9 288 Q0P8A9
284 A0A077ZHN8 289 A0A077ZHN8
285 A0A077ZFY8 290 A0A077ZFY8
286 M5B8V9 291 M5B8V9
287 M5BAG7 292 M5BAG7
288 S0DS17 293 S0DS17
289 .... 294 ....
290 295
291 ----- 296 -----
292 297
293 **MAP OUTPUT EXAMPLES** 298 **MAP OUTPUT EXAMPLES**
294 299