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comparison uniprot.xml @ 0:48522382b6a4 draft

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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
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children cd2a41c65447
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-1:000000000000 0:48522382b6a4
1 <tool id="uniprot" name="UniProt" version="0.1">
2 <description>ID mapping and retrieval</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="2.7">requests</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 <regex match="Error:" />
13 <regex match="Exception:" />
14 </stdio>
15 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command>
16 <command><![CDATA[
17
18 cut -f ${id_column} $infile > id_file.tabular &&
19
20 $__tool_directory__/uniprot.py
21
22 #if $tool.tool_choice == "retrieve":
23 retrieve -f $tool.format $infile ./output
24 #elif $tool.tool_choice == "map":
25 map
26
27 #if $tool.from.category_FROM == "uniprot":
28 $tool.from.db_uniprot_FROM
29 #elif $tool.from.category_FROM == "oseqdb":
30 $tool.from.db_oseqdb
31 #elif $tool.from.category_FROM == "3Dstrdb":
32 $tool.from.db_3Dstrdb
33 #elif $tool.from.category_FROM == "ppidb":
34 $tool.from.db_ppidb
35 #elif $tool.from.category_FROM == "chemistry":
36 $tool.from.db_chemistry
37 #elif $tool.from.category_FROM == "protfgdb":
38 $tool.from.db_protfgdb
39 #elif $tool.from.category_FROM == "polymorphismANDmutation":
40 $tool.from.db_polymorphismANDmutation
41 #elif $tool.from.category_FROM == "db_2DgelDB":
42 $tool.from.db_2DgelDB
43 #elif $tool.from.category_FROM == "ProtocolsMaterialsDB":
44 $tool.from.ProtocolsMaterialsDB
45 #elif $tool.from.category_FROM == "db_GenomeAnnotationDB":
46 $tool.from.db_GenomeAnnotationDB
47 #elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB":
48 $tool.from.db_OrganismSpecificGeneDB
49 #elif $tool.from.category_FROM == "db_phylogenomic":
50 $tool.from.db_phylogenomic
51 #elif $tool.from.category_FROM == "db_EnzymePathwayDB":
52 $tool.from.db_EnzymePathwayDB
53 #elif $tool.from.category_FROM == "db_GeneExpression":
54 $tool.from.db_GeneExpression
55 #elif $tool.from.category_FROM == "db_other":
56 $tool.from.db_other
57 #end if
58
59 #if $tool.to.category_TO == "uniprot":
60 $tool.to.db_uniprot_TO
61 #elif $tool.to.category_TO == "oseqdb":
62 $tool.to.db_oseqdb
63 #elif $tool.to.category_TO == "3Dstrdb":
64 $tool.to.db_3Dstrdb
65 #elif $tool.to.category_TO == "ppidb":
66 $tool.to.db_ppidb
67 #elif $tool.to.category_TO == "chemistry":
68 $tool.to.db_chemistry
69 #elif $tool.to.category_TO == "protfgdb":
70 $tool.to.db_protfgdb
71 #elif $tool.to.category_TO == "polymorphismANDmutation":
72 $tool.to.db_polymorphismANDmutation
73 #elif $tool.to.category_TO == "db_2DgelDB":
74 $tool.to.db_2DgelDB
75 #elif $tool.to.category_TO == "ProtocolsMaterialsDB":
76 $tool.to.ProtocolsMaterialsDB
77 #elif $tool.to.category_TO == "db_GenomeAnnotationDB":
78 $tool.to.db_GenomeAnnotationDB
79 #elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB":
80 $tool.to.db_OrganismSpecificGeneDB
81 #elif $tool.to.category_TO == "db_phylogenomic":
82 $tool.to.db_phylogenomic
83 #elif $tool.to.category_TO == "db_EnzymePathwayDB":
84 $tool.to.db_EnzymePathwayDB
85 #elif $tool.to.category_TO == "db_GeneExpression":
86 $tool.to.db_GeneExpression
87 #elif $tool.to.category_TO == "db_other":
88 $tool.to.db_other
89 #end if
90
91 id_file.tabular
92 ./output
93 #end if
94
95 ]]></command>
96 <inputs>
97 <param name="infile" type="data" format="tabular" label="Input file with IDs"
98 help="One ID in each line."/>
99 <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/>
100
101 <conditional name="tool">
102 <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help="">
103 <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option>
104 <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option>
105 </param>
106 <when value="map">
107 <conditional name="from">
108 <expand macro="macro-category_FROM"/>
109 <when value="uniprot">
110 <expand macro="macro-db_uniprot_FROM"/>
111 </when>
112 <when value="oseqdb">
113 <expand macro="macro-db_oseqdb"/>
114 </when>
115 <when value="3Dstrdb">
116 <expand macro="macro-db_3Dstrdb"/>
117 </when>
118 <when value="ppidb">
119 <expand macro="macro-db_ppidb"/>
120 </when>
121 <when value="chemistry">
122 <expand macro="macro-db_chemistry"/>
123 </when>
124 <when value="protfgdb">
125 <expand macro="macro-db_protfgdb"/>
126 </when>
127 <when value="polymorphismANDmutation">
128 <expand macro="macro-db_polymorphismANDmutation"/>
129 </when>
130 <when value="2DgelDB">
131 <expand macro="macro-db_2DgelDB"/>
132 </when>
133 <when value="ProtocolsMaterialsDB">
134 <expand macro="macro-db_ProtocolsMaterialsDB"/>
135 </when>
136 <when value="GenomeAnnotationDB">
137 <expand macro="macro-db_GenomeAnnotationDB"/>
138 </when>
139 <when value="OrganismSpecificGeneDB">
140 <expand macro="macro-db_OrganismSpecificGeneDB"/>
141 </when>
142 <when value="phylogenomic">
143 <expand macro="macro-db_phylogenomic"/>
144 </when>
145 <when value="EnzymePathwayDB">
146 <expand macro="macro-db_EnzymePathwayDB"/>
147 </when>
148 <when value="GeneExpression">
149 <expand macro="macro-db_GeneExpression"/>
150 </when>
151 <when value="other">
152 <expand macro="macro-db_other"/>
153 </when>
154 </conditional>
155 <conditional name="to">
156 <expand macro="macro-category_TO"/>
157 <when value="uniprot">
158 <expand macro="macro-db_uniprot_TO"/>
159 </when>
160 <when value="oseqdb">
161 <expand macro="macro-db_oseqdb"/>
162 </when>
163 <when value="3Dstrdb">
164 <expand macro="macro-db_3Dstrdb"/>
165 </when>
166 <when value="ppidb">
167 <expand macro="macro-db_ppidb"/>
168 </when>
169 <when value="chemistry">
170 <expand macro="macro-db_chemistry"/>
171 </when>
172 <when value="protfgdb">
173 <expand macro="macro-db_protfgdb"/>
174 </when>
175 <when value="polymorphismANDmutation">
176 <expand macro="macro-db_polymorphismANDmutation"/>
177 </when>
178 <when value="2DgelDB">
179 <expand macro="macro-db_2DgelDB"/>
180 </when>
181 <when value="ProtocolsMaterialsDB">
182 <expand macro="macro-db_ProtocolsMaterialsDB"/>
183 </when>
184 <when value="GenomeAnnotationDB">
185 <expand macro="macro-db_GenomeAnnotationDB"/>
186 </when>
187 <when value="OrganismSpecificGeneDB">
188 <expand macro="macro-db_OrganismSpecificGeneDB"/>
189 </when>
190 <when value="phylogenomic">
191 <expand macro="macro-db_phylogenomic"/>
192 </when>
193 <when value="EnzymePathwayDB">
194 <expand macro="macro-db_EnzymePathwayDB"/>
195 </when>
196 <when value="GeneExpression">
197 <expand macro="macro-db_GeneExpression"/>
198 </when>
199 <when value="other">
200 <expand macro="macro-db_other"/>
201 </when>
202 </conditional>
203 </when>
204 <when value="retrieve">
205 <param name="format" type="select" label="Choose format of output file" help="">
206 <option value="fasta">fasta</option>
207 <option value="gff">gff</option>
208 </param>
209 </when>
210 </conditional>
211
212 </inputs>
213 <outputs>
214 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
215 label="${tool.name} on ${on_string} (retrieve output)">
216 <filter>tool['tool_choice'] == 'retrieve'</filter>
217 <filter>tool['format'] == 'fasta'</filter>
218 </data>
219 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
220 label="${tool.name} on ${on_string} (retrieve output)">
221 <filter>tool['tool_choice'] == 'retrieve'</filter>
222 <filter>tool['format'] == 'gff'</filter>
223 </data>
224 <data name="outfile_map" format="tabular" from_work_dir="./output"
225 label="${tool.name} on ${on_string} (map output)">
226 <filter>tool['tool_choice'] == 'map'</filter>
227 </data>
228 </outputs>
229 <tests>
230 <test>
231 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
232 <param name="id_column" value="c1"/>
233 <param name="format" value="fasta"/>
234 <param name="tool_choice" value="retrieve"/>
235 <output name="outfile_retrieve" file="test1_retrieve.fasta" ftype="fasta"/>
236 </test>
237 <test>
238 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
239 <param name="id_column" value="c1"/>
240 <param name="format" value="gff"/>
241 <param name="tool_choice" value="retrieve"/>
242 <output name="outfile_retrieve" file="test2_retrieve.gff" ftype="gff"/>
243 </test>
244 <test>
245 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
246 <param name="id_column" value="c1"/>
247 <param name="tool_choice" value="map"/>
248 <param name="category_FROM" value="uniprot"/>
249 <param name="db_uniprot_FROM" value="ID"/>
250 <param name="category_TO" value="uniprot"/>
251 <param name="db_uniprot_TO" value="GENENAME"/>
252 <output name="outfile_map" file="test1_map.tab" ftype="tabular"/>
253 </test>
254 <test>
255 <param name="infile" value="id_map_refseq.txt" ftype="tabular"/>
256 <param name="id_column" value="c1"/>
257 <param name="tool_choice" value="map"/>
258 <param name="category_FROM" value="oseqdb"/>
259 <param name="db_oseqdb" value="REFSEQ_NT_ID"/>
260 <param name="category_TO" value="uniprot"/>
261 <param name="db_uniprot_TO" value="ID"/>
262 <output name="outfile_map" file="test2_map.tab" ftype="tabular"/>
263 </test>
264 </tests>
265 <help><![CDATA[
266
267 .. class:: infomark
268
269 **What it does**
270
271 This tool provides access to the UniProt API. You can retrieve sequence informations given a list of sequence identifiers or map
272 identifiers between different databases.
273 Hence, this tool offers you two modes: *map* and *retrieve*.
274
275 -----
276
277 **INPUT**
278
279 The input is a list of IDs.
280
281 *example*:
282
283 Q0P8A9
284 A0A077ZHN8
285 A0A077ZFY8
286 M5B8V9
287 M5BAG7
288 S0DS17
289 ....
290
291 -----
292
293 **MAP OUTPUT EXAMPLES**
294
295 FROM refseq TO embl::
296
297 From To
298 NM_130786 A1BG_HUMAN
299 NM_130786 V9HWD8_HUMAN
300 NM_001087 A0A024R410_HUMAN
301 NM_001087 AAMP_HUMAN
302
303 FROM uniprot TO genename::
304
305 From To
306 Q0P8A9 fdhC
307 A0A077ZHN8 TTRE_0000819801
308 A0A077ZFY8 TTRE_0000758701
309 M5B8V9 CMN_01519
310 M5BAG7 cydC
311 S0DS17 FFUJ_00006
312 A0A077Z587 TTRE_0000309301
313 Q13685 AAMP
314 O14639 ABLIM1
315
316 -----
317
318 **RETRIEVE OUTPUT EXAMPLES**
319
320 retrieve gff::
321
322 #gff-version 3
323 #sequence-region S0DS17 1 369
324 #sequence-region M5BAG7 1 563
325 #sequence-region A0A077Z587 1 772
326 #sequence-region A0A077ZFY8 1 973
327 #sequence-region O14639 1 778
328 O14639 UniProtKB Chain 1 778 . . . ID=PRO_0000075697;Note=Actin-binding LIM protein 1
329 O14639 UniProtKB Domain 97 156 . . . Note=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125
330 O14639 UniProtKB Domain 156 216 . . . Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125
331 O14639 Un...
332
333 retrieve fasta::
334
335 >tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1
336 MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS
337 YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKY...
338 >tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1
339 MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG
340 VRAFALGRAAFRYLERITSHDAAFRALATLRV...
341 >tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1
342 MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD
343 VIKDVNGSRIDSRELCRDLIRTHKVLTV...
344
345 -----
346
347 This tool is based on the work `Jan Rudolph`_ and the UniProt API.
348
349 .. _Jan Rudolph: https://github.com/jdrudolph/uniprot
350
351 ]]></help>
352 <citations>
353 <citation type="doi">10.1093/nar/gku989</citation>
354 </citations>
355 </tool>