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comparison macros.xml @ 0:71bcf87a7031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:39:36 -0400
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1 <?xml version="1.0"?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">1.1</token>
4 <token name="@EMAIL_ARGUMENTS@">
5 --user_email "$__user_email__"
6 #set admin_emails = ';'.join(str($__admin_users__).split(','))
7 --admin_email "$admin_emails"
8 </token>
9 <!-- TODO: citation -->
10 <token name="@REFERENCES@"><![CDATA[
11 ]]></token>
12 <token name="@DISCLAIMER@"><![CDATA[
13 Usage Guidelines and Requirements
14 =================================
15
16 Frequency, Timing, and Registration of E-utility URL Requests
17 -------------------------------------------------------------
18
19 In order not to overload the E-utility servers, NCBI recommends that users
20 limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time
21 during weekdays. Failure to comply with this policy may result in an IP address
22 being blocked from accessing NCBI.
23
24 Minimizing the Number of Requests
25 ---------------------------------
26
27 If a task requires searching for and/or downloading a large number of
28 records, it is much more efficient to use the Entrez History to upload
29 and/or retrieve these records in batches rather than using separate
30 requests for each record. Please refer to Application 3 in Chapter 3
31 for an example. Many thousands of IDs can be uploaded using a single
32 EPost request, and several hundred records can be downloaded using one
33 EFetch request.
34
35
36 Disclaimer and Copyright Issues
37 -------------------------------
38
39 In accordance with requirements of NCBI's E-Utilities, we must provide
40 the following disclaimer:
41
42 Please note that abstracts in PubMed may incorporate material that may
43 be protected by U.S. and foreign copyright laws. All persons
44 reproducing, redistributing, or making commercial use of this
45 information are expected to adhere to the terms and conditions asserted
46 by the copyright holder. Transmission or reproduction of protected
47 items beyond that allowed by fair use (PDF) as defined in the copyright
48 laws requires the written permission of the copyright owners. NLM
49 provides no legal advice concerning distribution of copyrighted
50 materials. Please consult your legal counsel. If you wish to do a large
51 data mining project on PubMed data, you can enter into a licensing
52 agreement and lease the data for free from NLM. For more information on
53 this please see `http://www.nlm.nih.gov/databases/leased.html <http://www.nlm.nih.gov/databases/leased.html>`__
54
55 The `full disclaimer <http://www.ncbi.nlm.nih.gov/About/disclaimer.html>`__ is available on
56 their website
57
58 Liability
59 ~~~~~~~~~
60
61 For documents and software available from this server, the
62 U.S. Government does not warrant or assume any legal liability or
63 responsibility for the accuracy, completeness, or usefulness of any
64 information, apparatus, product, or process disclosed.
65
66 Endorsement
67 ~~~~~~~~~~~
68
69 NCBI does not endorse or recommend any commercial
70 products, processes, or services. The views and opinions of authors
71 expressed on NCBI's Web sites do not necessarily state or reflect those
72 of the U.S. Government, and they may not be used for advertising or
73 product endorsement purposes.
74
75 External Links
76 ~~~~~~~~~~~~~~
77
78 Some NCBI Web pages may provide links to other Internet
79 sites for the convenience of users. NCBI is not responsible for the
80 availability or content of these external sites, nor does NCBI endorse,
81 warrant, or guarantee the products, services, or information described
82 or offered at these other Internet sites. Users cannot assume that the
83 external sites will abide by the same Privacy Policy to which NCBI
84 adheres. It is the responsibility of the user to examine the copyright
85 and licensing restrictions of linked pages and to secure all necessary
86 permissions.
87 ]]></token>
88 <xml name="dbselect"
89 token_name="db_select"
90 token_label="NCBI Database to Use"
91 >
92 <param name="@NAME@" type="select" label="@LABEL@">
93 <option value="annotinfo">Annotation Information</option>
94 <option value="assembly">Assembly</option>
95 <option value="bioproject">BioProject</option>
96 <option value="biosample">BioSample</option>
97 <option value="biosystems">Biosystems</option>
98 <option value="blastdbinfo">Blast Database Information</option>
99 <option value="books">Books</option>
100 <option value="cdd">Conserved Domains</option>
101 <option value="clinvar">Clinical Variants</option>
102 <option value="clone">CLone</option>
103 <option value="dbvar">dbVar</option>
104 <option value="gap">dbGaP</option>
105 <option value="gapplus">gapplus</option>
106 <option value="gds">GEO Datasets</option>
107 <option value="gencoll">Gencoll</option>
108 <option value="gene">Gene</option>
109 <option value="genome">Genome</option>
110 <option value="geoprofiles">GEO Profiles</option>
111 <option value="grasp">grasp</option>
112 <option value="gtr">Genetic Testing Registry</option>
113 <option value="homologene">HomoloGene</option>
114 <option value="medgen">MedGen</option>
115 <option value="mesh">MeSH</option>
116 <option value="ncbisearch">NCBI Web Site</option>
117 <option value="nlmcatalog">NLM Catalog</option>
118 <option value="nuccore">Nuccore</option>
119 <option value="nucest">EST</option>
120 <option value="nucgss">GSS</option>
121 <option value="nucleotide">Nucleotide</option>
122 <option value="omim">OMIM</option>
123 <option value="orgtrack">Orgtrack</option>
124 <option value="pcassay">PubChem BioAssay</option>
125 <option value="pccompound">PubChem Compound</option>
126 <option value="pcsubstance">PubChem Substance</option>
127 <option value="pmc">PubMed Central</option>
128 <option value="popset">PopSet</option>
129 <option value="probe">Probe</option>
130 <option value="protein">Protein</option>
131 <option value="proteinclusters">Protein Clusters</option>
132 <option value="pubmed">PubMed</option>
133 <option value="pubmedhealth">PubMed Health</option>
134 <option value="seqannot">seqannot</option>
135 <option value="snp">SNP</option>
136 <option value="sra">SRA</option>
137 <option value="structure">Structure</option>
138 <option value="taxonomy">Taxonomy</option>
139 <option value="unigene">UniGene</option>
140 </param>
141 </xml>
142 <xml name="db">
143 <conditional name="db">
144 <expand macro="dbselect" />
145 <when value="annotinfo">
146 <param name="output_format" type="select" label="Output Format">
147 <option value="docsum-json">Document Summary (json)</option>
148 <option value="docsum-xml">Document Summary (xml)</option>
149 <option value="full-text">Full Document (text)</option>
150 <option value="full-xml">Full Document (xml)</option>
151 <option value="uilist-text">Unique Identifier List (text)</option>
152 <option value="uilist-xml">Unique Identifier List (xml)</option>
153 </param>
154 </when>
155 <when value="assembly">
156 <param name="output_format" type="select" label="Output Format">
157 <option value="docsum-json">Document Summary (json)</option>
158 <option value="docsum-xml">Document Summary (xml)</option>
159 <option value="full-text">Full Document (text)</option>
160 <option value="full-xml">Full Document (xml)</option>
161 <option value="uilist-text">Unique Identifier List (text)</option>
162 <option value="uilist-xml">Unique Identifier List (xml)</option>
163 </param>
164 </when>
165 <when value="bioproject">
166 <param name="output_format" type="select" label="Output Format">
167 <option value="docsum-json">Document Summary (json)</option>
168 <option value="docsum-xml">Document Summary (xml)</option>
169 <option value="full-text">Full Document (text)</option>
170 <option value="full-xml">Full Document (xml)</option>
171 <option value="native-None">BioProject Report</option>
172 <option value="native-xml">RecordSet (xml)</option>
173 <option value="uilist-text">Unique Identifier List (text)</option>
174 <option value="uilist-xml">Unique Identifier List (xml)</option>
175 </param>
176 </when>
177 <when value="biosample">
178 <param name="output_format" type="select" label="Output Format">
179 <option value="docsum-json">Document Summary (json)</option>
180 <option value="docsum-xml">Document Summary (xml)</option>
181 <option value="full-text">Full Document (text)</option>
182 <option value="full-xml">Full Document (xml)</option>
183 <option value="native-None">BioSample Report</option>
184 <option value="native-xml">BioSampleSet (xml)</option>
185 <option value="uilist-text">Unique Identifier List (text)</option>
186 <option value="uilist-xml">Unique Identifier List (xml)</option>
187 </param>
188 </when>
189 <when value="biosystems">
190 <param name="output_format" type="select" label="Output Format">
191 <option value="docsum-json">Document Summary (json)</option>
192 <option value="docsum-xml">Document Summary (xml)</option>
193 <option value="full-text">Full Document (text)</option>
194 <option value="full-xml">Full Document (xml)</option>
195 <option value="native-xml">Sys-set (xml)</option>
196 <option value="uilist-text">Unique Identifier List (text)</option>
197 <option value="uilist-xml">Unique Identifier List (xml)</option>
198 </param>
199 </when>
200 <when value="blastdbinfo">
201 <param name="output_format" type="select" label="Output Format">
202 <option value="docsum-json">Document Summary (json)</option>
203 <option value="docsum-xml">Document Summary (xml)</option>
204 <option value="full-text">Full Document (text)</option>
205 <option value="full-xml">Full Document (xml)</option>
206 <option value="uilist-text">Unique Identifier List (text)</option>
207 <option value="uilist-xml">Unique Identifier List (xml)</option>
208 </param>
209 </when>
210 <when value="books">
211 <param name="output_format" type="select" label="Output Format">
212 <option value="docsum-json">Document Summary (json)</option>
213 <option value="docsum-xml">Document Summary (xml)</option>
214 <option value="full-text">Full Document (text)</option>
215 <option value="full-xml">Full Document (xml)</option>
216 <option value="uilist-text">Unique Identifier List (text)</option>
217 <option value="uilist-xml">Unique Identifier List (xml)</option>
218 </param>
219 </when>
220 <when value="cdd">
221 <param name="output_format" type="select" label="Output Format">
222 <option value="docsum-json">Document Summary (json)</option>
223 <option value="docsum-xml">Document Summary (xml)</option>
224 <option value="full-text">Full Document (text)</option>
225 <option value="full-xml">Full Document (xml)</option>
226 <option value="uilist-text">Unique Identifier List (text)</option>
227 <option value="uilist-xml">Unique Identifier List (xml)</option>
228 </param>
229 </when>
230 <when value="clinvar">
231 <param name="output_format" type="select" label="Output Format">
232 <option value="docsum-json">Document Summary (json)</option>
233 <option value="docsum-xml">Document Summary (xml)</option>
234 <option value="full-text">Full Document (text)</option>
235 <option value="full-xml">Full Document (xml)</option>
236 <option value="uilist-text">Unique Identifier List (text)</option>
237 <option value="uilist-xml">Unique Identifier List (xml)</option>
238 </param>
239 </when>
240 <when value="clone">
241 <param name="output_format" type="select" label="Output Format">
242 <option value="docsum-json">Document Summary (json)</option>
243 <option value="docsum-xml">Document Summary (xml)</option>
244 <option value="full-text">Full Document (text)</option>
245 <option value="full-xml">Full Document (xml)</option>
246 <option value="uilist-text">Unique Identifier List (text)</option>
247 <option value="uilist-xml">Unique Identifier List (xml)</option>
248 </param>
249 </when>
250 <when value="dbvar">
251 <param name="output_format" type="select" label="Output Format">
252 <option value="docsum-json">Document Summary (json)</option>
253 <option value="docsum-xml">Document Summary (xml)</option>
254 <option value="full-text">Full Document (text)</option>
255 <option value="full-xml">Full Document (xml)</option>
256 <option value="uilist-text">Unique Identifier List (text)</option>
257 <option value="uilist-xml">Unique Identifier List (xml)</option>
258 </param>
259 </when>
260 <when value="gap">
261 <param name="output_format" type="select" label="Output Format">
262 <option value="docsum-json">Document Summary (json)</option>
263 <option value="docsum-xml">Document Summary (xml)</option>
264 <option value="full-text">Full Document (text)</option>
265 <option value="full-xml">Full Document (xml)</option>
266 <option value="uilist-text">Unique Identifier List (text)</option>
267 <option value="uilist-xml">Unique Identifier List (xml)</option>
268 </param>
269 </when>
270 <when value="gapplus">
271 <param name="output_format" type="select" label="Output Format">
272 <option value="docsum-json">Document Summary (json)</option>
273 <option value="docsum-xml">Document Summary (xml)</option>
274 <option value="full-text">Full Document (text)</option>
275 <option value="full-xml">Full Document (xml)</option>
276 <option value="uilist-text">Unique Identifier List (text)</option>
277 <option value="uilist-xml">Unique Identifier List (xml)</option>
278 </param>
279 </when>
280 <when value="gds">
281 <param name="output_format" type="select" label="Output Format">
282 <option value="docsum-json">Document Summary (json)</option>
283 <option value="docsum-xml">Document Summary (xml)</option>
284 <option value="full-text">Full Document (text)</option>
285 <option value="full-xml">Full Document (xml)</option>
286 <option value="native-xml">RecordSet (xml)</option>
287 <option value="summary-text">Summary (text)</option>
288 <option value="uilist-text">Unique Identifier List (text)</option>
289 <option value="uilist-xml">Unique Identifier List (xml)</option>
290 </param>
291 </when>
292 <when value="gencoll">
293 <param name="output_format" type="select" label="Output Format">
294 <option value="docsum-json">Document Summary (json)</option>
295 <option value="docsum-xml">Document Summary (xml)</option>
296 <option value="full-text">Full Document (text)</option>
297 <option value="full-xml">Full Document (xml)</option>
298 <option value="uilist-text">Unique Identifier List (text)</option>
299 <option value="uilist-xml">Unique Identifier List (xml)</option>
300 </param>
301 </when>
302 <when value="gene">
303 <param name="output_format" type="select" label="Output Format">
304 <option value="docsum-json">Document Summary (json)</option>
305 <option value="docsum-xml">Document Summary (xml)</option>
306 <option value="full-text">Full Document (text)</option>
307 <option value="full-xml">Full Document (xml)</option>
308 <option value="gene_table-xml">Gene Table (xml)</option>
309 <option value="native-asn.1">Entrezgene (asn.1)</option>
310 <option value="native-text">Gene Report (text)</option>
311 <option value="native-xml">Entrezgene-Set (xml)</option>
312 <option value="tabular-tabular">Tabular Report (tabular)</option>
313 <option value="uilist-text">Unique Identifier List (text)</option>
314 <option value="uilist-xml">Unique Identifier List (xml)</option>
315 </param>
316 </when>
317 <when value="genome">
318 <param name="output_format" type="select" label="Output Format">
319 <option value="docsum-json">Document Summary (json)</option>
320 <option value="docsum-xml">Document Summary (xml)</option>
321 <option value="full-text">Full Document (text)</option>
322 <option value="full-xml">Full Document (xml)</option>
323 <option value="uilist-text">Unique Identifier List (text)</option>
324 <option value="uilist-xml">Unique Identifier List (xml)</option>
325 </param>
326 </when>
327 <when value="geoprofiles">
328 <param name="output_format" type="select" label="Output Format">
329 <option value="docsum-json">Document Summary (json)</option>
330 <option value="docsum-xml">Document Summary (xml)</option>
331 <option value="full-text">Full Document (text)</option>
332 <option value="full-xml">Full Document (xml)</option>
333 <option value="uilist-text">Unique Identifier List (text)</option>
334 <option value="uilist-xml">Unique Identifier List (xml)</option>
335 </param>
336 </when>
337 <when value="grasp">
338 <param name="output_format" type="select" label="Output Format">
339 <option value="docsum-json">Document Summary (json)</option>
340 <option value="docsum-xml">Document Summary (xml)</option>
341 <option value="full-text">Full Document (text)</option>
342 <option value="full-xml">Full Document (xml)</option>
343 <option value="uilist-text">Unique Identifier List (text)</option>
344 <option value="uilist-xml">Unique Identifier List (xml)</option>
345 </param>
346 </when>
347 <when value="gtr">
348 <param name="output_format" type="select" label="Output Format">
349 <option value="docsum-json">Document Summary (json)</option>
350 <option value="docsum-xml">Document Summary (xml)</option>
351 <option value="full-text">Full Document (text)</option>
352 <option value="full-xml">Full Document (xml)</option>
353 <option value="uilist-text">Unique Identifier List (text)</option>
354 <option value="uilist-xml">Unique Identifier List (xml)</option>
355 </param>
356 </when>
357 <when value="homologene">
358 <param name="output_format" type="select" label="Output Format">
359 <option value="alignmentscores-text">Alignment Scores (text)</option>
360 <option value="docsum-json">Document Summary (json)</option>
361 <option value="docsum-xml">Document Summary (xml)</option>
362 <option value="fasta-fasta">FASTA (fasta)</option>
363 <option value="full-text">Full Document (text)</option>
364 <option value="full-xml">Full Document (xml)</option>
365 <option value="homologene-text">Homologene Report (text)</option>
366 <option value="native-asn.1">HG-Entry (asn.1)</option>
367 <option value="native-text">Homologene List (text)</option>
368 <option value="native-xml">Entrez-Homologene-Set (xml)</option>
369 <option value="uilist-text">Unique Identifier List (text)</option>
370 <option value="uilist-xml">Unique Identifier List (xml)</option>
371 </param>
372 </when>
373 <when value="medgen">
374 <param name="output_format" type="select" label="Output Format">
375 <option value="docsum-json">Document Summary (json)</option>
376 <option value="docsum-xml">Document Summary (xml)</option>
377 <option value="full-text">Full Document (text)</option>
378 <option value="full-xml">Full Document (xml)</option>
379 <option value="uilist-text">Unique Identifier List (text)</option>
380 <option value="uilist-xml">Unique Identifier List (xml)</option>
381 </param>
382 </when>
383 <when value="mesh">
384 <param name="output_format" type="select" label="Output Format">
385 <option value="docsum-json">Document Summary (json)</option>
386 <option value="docsum-xml">Document Summary (xml)</option>
387 <option value="full-text">Full Document (text)</option>
388 <option value="full-text">Full Record (text)</option>
389 <option value="full-xml">Full Document (xml)</option>
390 <option value="native-text">MeSH Report (text)</option>
391 <option value="native-xml">RecordSet (xml)</option>
392 <option value="uilist-text">Unique Identifier List (text)</option>
393 <option value="uilist-xml">Unique Identifier List (xml)</option>
394 </param>
395 </when>
396 <when value="ncbisearch">
397 <param name="output_format" type="select" label="Output Format">
398 <option value="docsum-json">Document Summary (json)</option>
399 <option value="docsum-xml">Document Summary (xml)</option>
400 <option value="full-text">Full Document (text)</option>
401 <option value="full-xml">Full Document (xml)</option>
402 <option value="uilist-text">Unique Identifier List (text)</option>
403 <option value="uilist-xml">Unique Identifier List (xml)</option>
404 </param>
405 </when>
406 <when value="nlmcatalog">
407 <param name="output_format" type="select" label="Output Format">
408 <option value="docsum-json">Document Summary (json)</option>
409 <option value="docsum-xml">Document Summary (xml)</option>
410 <option value="full-text">Full Document (text)</option>
411 <option value="full-xml">Full Document (xml)</option>
412 <option value="native-text">Full Record (text)</option>
413 <option value="native-xml">NLMCatalogRecordSet (xml)</option>
414 <option value="uilist-text">Unique Identifier List (text)</option>
415 <option value="uilist-xml">Unique Identifier List (xml)</option>
416 </param>
417 </when>
418 <when value="nuccore">
419 <param name="output_format" type="select" label="Output Format">
420 <option value="acc-text">Accession Number (text)</option>
421 <option value="docsum-json">Document Summary (json)</option>
422 <option value="docsum-xml">Document Summary (xml)</option>
423 <option value="est-xml">EST Report (xml)</option>
424 <option value="fasta-fasta">FASTA (fasta)</option>
425 <option value="fasta-xml">TinySeq (xml)</option>
426 <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
427 <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
428 <option value="ft-text">Feature Table (text)</option>
429 <option value="full-text">Full Document (text)</option>
430 <option value="full-xml">Full Document (xml)</option>
431 <option value="gb-text">GenBank Flatfile (text)</option>
432 <option value="gb-xml">GBSet (xml)</option>
433 <option value="gbc-xml">INSDSet (xml)</option>
434 <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
435 <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
436 <option value="gp-text">GenPept Flatfile (text)</option>
437 <option value="gp-xml">GBSet (xml)</option>
438 <option value="gpc-xml">INSDSet (xml)</option>
439 <option value="gss-text">GSS Report (text)</option>
440 <option value="ipg-text">Identical Protein Report (text)</option>
441 <option value="ipg-xml">IPGReportSet (xml)</option>
442 <option value="native-text">Seq-entry (text)</option>
443 <option value="native-xml">Bioseq-set (xml)</option>
444 <option value="seqid-asn.1">Seq-id (asn.1)</option>
445 <option value="uilist-text">Unique Identifier List (text)</option>
446 <option value="uilist-xml">Unique Identifier List (xml)</option>
447 </param>
448 </when>
449 <when value="nucest">
450 <param name="output_format" type="select" label="Output Format">
451 <option value="acc-text">Accession Number (text)</option>
452 <option value="docsum-json">Document Summary (json)</option>
453 <option value="docsum-xml">Document Summary (xml)</option>
454 <option value="est-xml">EST Report (xml)</option>
455 <option value="fasta-fasta">FASTA (fasta)</option>
456 <option value="fasta-xml">TinySeq (xml)</option>
457 <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
458 <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
459 <option value="ft-text">Feature Table (text)</option>
460 <option value="full-text">Full Document (text)</option>
461 <option value="full-xml">Full Document (xml)</option>
462 <option value="gb-text">GenBank Flatfile (text)</option>
463 <option value="gb-xml">GBSet (xml)</option>
464 <option value="gbc-xml">INSDSet (xml)</option>
465 <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
466 <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
467 <option value="gp-text">GenPept Flatfile (text)</option>
468 <option value="gp-xml">GBSet (xml)</option>
469 <option value="gpc-xml">INSDSet (xml)</option>
470 <option value="gss-text">GSS Report (text)</option>
471 <option value="ipg-text">Identical Protein Report (text)</option>
472 <option value="ipg-xml">IPGReportSet (xml)</option>
473 <option value="native-text">Seq-entry (text)</option>
474 <option value="native-xml">Bioseq-set (xml)</option>
475 <option value="seqid-asn.1">Seq-id (asn.1)</option>
476 <option value="uilist-text">Unique Identifier List (text)</option>
477 <option value="uilist-xml">Unique Identifier List (xml)</option>
478 </param>
479 </when>
480 <when value="nucgss">
481 <param name="output_format" type="select" label="Output Format">
482 <option value="acc-text">Accession Number (text)</option>
483 <option value="docsum-json">Document Summary (json)</option>
484 <option value="docsum-xml">Document Summary (xml)</option>
485 <option value="est-xml">EST Report (xml)</option>
486 <option value="fasta-fasta">FASTA (fasta)</option>
487 <option value="fasta-xml">TinySeq (xml)</option>
488 <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
489 <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
490 <option value="ft-text">Feature Table (text)</option>
491 <option value="full-text">Full Document (text)</option>
492 <option value="full-xml">Full Document (xml)</option>
493 <option value="gb-text">GenBank Flatfile (text)</option>
494 <option value="gb-xml">GBSet (xml)</option>
495 <option value="gbc-xml">INSDSet (xml)</option>
496 <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
497 <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
498 <option value="gp-text">GenPept Flatfile (text)</option>
499 <option value="gp-xml">GBSet (xml)</option>
500 <option value="gpc-xml">INSDSet (xml)</option>
501 <option value="gss-text">GSS Report (text)</option>
502 <option value="ipg-text">Identical Protein Report (text)</option>
503 <option value="ipg-xml">IPGReportSet (xml)</option>
504 <option value="native-text">Seq-entry (text)</option>
505 <option value="native-xml">Bioseq-set (xml)</option>
506 <option value="seqid-asn.1">Seq-id (asn.1)</option>
507 <option value="uilist-text">Unique Identifier List (text)</option>
508 <option value="uilist-xml">Unique Identifier List (xml)</option>
509 </param>
510 </when>
511 <when value="nucleotide">
512 <param name="output_format" type="select" label="Output Format">
513 <option value="acc-text">Accession Number (text)</option>
514 <option value="docsum-json">Document Summary (json)</option>
515 <option value="docsum-xml">Document Summary (xml)</option>
516 <option value="est-xml">EST Report (xml)</option>
517 <option value="fasta-fasta">FASTA (fasta)</option>
518 <option value="fasta-xml">TinySeq (xml)</option>
519 <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
520 <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
521 <option value="ft-text">Feature Table (text)</option>
522 <option value="full-text">Full Document (text)</option>
523 <option value="full-xml">Full Document (xml)</option>
524 <option value="gb-text">GenBank Flatfile (text)</option>
525 <option value="gb-xml">GBSet (xml)</option>
526 <option value="gbc-xml">INSDSet (xml)</option>
527 <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
528 <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
529 <option value="gp-text">GenPept Flatfile (text)</option>
530 <option value="gp-xml">GBSet (xml)</option>
531 <option value="gpc-xml">INSDSet (xml)</option>
532 <option value="gss-text">GSS Report (text)</option>
533 <option value="ipg-text">Identical Protein Report (text)</option>
534 <option value="ipg-xml">IPGReportSet (xml)</option>
535 <option value="native-text">Seq-entry (text)</option>
536 <option value="native-xml">Bioseq-set (xml)</option>
537 <option value="seqid-asn.1">Seq-id (asn.1)</option>
538 <option value="uilist-text">Unique Identifier List (text)</option>
539 <option value="uilist-xml">Unique Identifier List (xml)</option>
540 </param>
541 </when>
542 <when value="omim">
543 <param name="output_format" type="select" label="Output Format">
544 <option value="docsum-json">Document Summary (json)</option>
545 <option value="docsum-xml">Document Summary (xml)</option>
546 <option value="full-text">Full Document (text)</option>
547 <option value="full-xml">Full Document (xml)</option>
548 <option value="uilist-text">Unique Identifier List (text)</option>
549 <option value="uilist-xml">Unique Identifier List (xml)</option>
550 </param>
551 </when>
552 <when value="orgtrack">
553 <param name="output_format" type="select" label="Output Format">
554 <option value="docsum-json">Document Summary (json)</option>
555 <option value="docsum-xml">Document Summary (xml)</option>
556 <option value="full-text">Full Document (text)</option>
557 <option value="full-xml">Full Document (xml)</option>
558 <option value="uilist-text">Unique Identifier List (text)</option>
559 <option value="uilist-xml">Unique Identifier List (xml)</option>
560 </param>
561 </when>
562 <when value="pcassay">
563 <param name="output_format" type="select" label="Output Format">
564 <option value="docsum-json">Document Summary (json)</option>
565 <option value="docsum-xml">Document Summary (xml)</option>
566 <option value="full-text">Full Document (text)</option>
567 <option value="full-xml">Full Document (xml)</option>
568 <option value="uilist-text">Unique Identifier List (text)</option>
569 <option value="uilist-xml">Unique Identifier List (xml)</option>
570 </param>
571 </when>
572 <when value="pccompound">
573 <param name="output_format" type="select" label="Output Format">
574 <option value="docsum-json">Document Summary (json)</option>
575 <option value="docsum-xml">Document Summary (xml)</option>
576 <option value="full-text">Full Document (text)</option>
577 <option value="full-xml">Full Document (xml)</option>
578 <option value="uilist-text">Unique Identifier List (text)</option>
579 <option value="uilist-xml">Unique Identifier List (xml)</option>
580 </param>
581 </when>
582 <when value="pcsubstance">
583 <param name="output_format" type="select" label="Output Format">
584 <option value="docsum-json">Document Summary (json)</option>
585 <option value="docsum-xml">Document Summary (xml)</option>
586 <option value="full-text">Full Document (text)</option>
587 <option value="full-xml">Full Document (xml)</option>
588 <option value="uilist-text">Unique Identifier List (text)</option>
589 <option value="uilist-xml">Unique Identifier List (xml)</option>
590 </param>
591 </when>
592 <when value="pmc">
593 <param name="output_format" type="select" label="Output Format">
594 <option value="docsum-json">Document Summary (json)</option>
595 <option value="docsum-xml">Document Summary (xml)</option>
596 <option value="full-text">Full Document (text)</option>
597 <option value="full-xml">Full Document (xml)</option>
598 <option value="medline-text">MEDLINE (text)</option>
599 <option value="native-xml">pmc-articleset (xml)</option>
600 <option value="uilist-text">Unique Identifier List (text)</option>
601 <option value="uilist-xml">Unique Identifier List (xml)</option>
602 </param>
603 </when>
604 <when value="popset">
605 <param name="output_format" type="select" label="Output Format">
606 <option value="docsum-json">Document Summary (json)</option>
607 <option value="docsum-xml">Document Summary (xml)</option>
608 <option value="full-text">Full Document (text)</option>
609 <option value="full-xml">Full Document (xml)</option>
610 <option value="uilist-text">Unique Identifier List (text)</option>
611 <option value="uilist-xml">Unique Identifier List (xml)</option>
612 </param>
613 </when>
614 <when value="probe">
615 <param name="output_format" type="select" label="Output Format">
616 <option value="docsum-json">Document Summary (json)</option>
617 <option value="docsum-xml">Document Summary (xml)</option>
618 <option value="full-text">Full Document (text)</option>
619 <option value="full-xml">Full Document (xml)</option>
620 <option value="uilist-text">Unique Identifier List (text)</option>
621 <option value="uilist-xml">Unique Identifier List (xml)</option>
622 </param>
623 </when>
624 <when value="protein">
625 <param name="output_format" type="select" label="Output Format">
626 <option value="docsum-json">Document Summary (json)</option>
627 <option value="docsum-xml">Document Summary (xml)</option>
628 <option value="full-text">Full Document (text)</option>
629 <option value="full-xml">Full Document (xml)</option>
630 <option value="uilist-text">Unique Identifier List (text)</option>
631 <option value="uilist-xml">Unique Identifier List (xml)</option>
632 </param>
633 </when>
634 <when value="proteinclusters">
635 <param name="output_format" type="select" label="Output Format">
636 <option value="docsum-json">Document Summary (json)</option>
637 <option value="docsum-xml">Document Summary (xml)</option>
638 <option value="full-text">Full Document (text)</option>
639 <option value="full-xml">Full Document (xml)</option>
640 <option value="uilist-text">Unique Identifier List (text)</option>
641 <option value="uilist-xml">Unique Identifier List (xml)</option>
642 </param>
643 </when>
644 <when value="pubmed">
645 <param name="output_format" type="select" label="Output Format">
646 <option value="abstract-xml">Abstract (xml)</option>
647 <option value="docsum-json">Document Summary (json)</option>
648 <option value="docsum-xml">Document Summary (xml)</option>
649 <option value="full-text">Full Document (text)</option>
650 <option value="full-xml">Full Document (xml)</option>
651 <option value="medline-text">MEDLINE (text)</option>
652 <option value="native-asn.1">Pubmed-entry (asn.1)</option>
653 <option value="native-xml">PubmedArticleSet (xml)</option>
654 <option value="uilist-text">Unique Identifier List (text)</option>
655 <option value="uilist-xml">Unique Identifier List (xml)</option>
656 </param>
657 </when>
658 <when value="pubmedhealth">
659 <param name="output_format" type="select" label="Output Format">
660 <option value="docsum-json">Document Summary (json)</option>
661 <option value="docsum-xml">Document Summary (xml)</option>
662 <option value="full-text">Full Document (text)</option>
663 <option value="full-xml">Full Document (xml)</option>
664 <option value="uilist-text">Unique Identifier List (text)</option>
665 <option value="uilist-xml">Unique Identifier List (xml)</option>
666 </param>
667 </when>
668 <when value="seqannot">
669 <param name="output_format" type="select" label="Output Format">
670 <option value="docsum-json">Document Summary (json)</option>
671 <option value="docsum-xml">Document Summary (xml)</option>
672 <option value="full-text">Full Document (text)</option>
673 <option value="full-xml">Full Document (xml)</option>
674 <option value="uilist-text">Unique Identifier List (text)</option>
675 <option value="uilist-xml">Unique Identifier List (xml)</option>
676 </param>
677 </when>
678 <when value="snp">
679 <param name="output_format" type="select" label="Output Format">
680 <option value="chr-text">Chromosome Report (text)</option>
681 <option value="docset-text">Summary (text)</option>
682 <option value="docsum-json">Document Summary (json)</option>
683 <option value="docsum-xml">Document Summary (xml)</option>
684 <option value="fasta-fasta">FASTA (fasta)</option>
685 <option value="flt-text">Flat File (text)</option>
686 <option value="full-text">Full Document (text)</option>
687 <option value="full-xml">Full Document (xml)</option>
688 <option value="native-asn.1">Rs (asn.1)</option>
689 <option value="native-xml">ExchangeSet (xml)</option>
690 <option value="rsr-tabular">RS Cluster Report (tabular)</option>
691 <option value="ssexemplar-text">SS Exemplar List (text)</option>
692 <option value="uilist-text">Unique Identifier List (text)</option>
693 <option value="uilist-xml">Unique Identifier List (xml)</option>
694 </param>
695 </when>
696 <when value="sra">
697 <param name="output_format" type="select" label="Output Format">
698 <option value="docsum-json">Document Summary (json)</option>
699 <option value="docsum-xml">Document Summary (xml)</option>
700 <option value="full-text">Full Document (text)</option>
701 <option value="full-xml">Full Document (xml)</option>
702 <option value="native-xml">EXPERIMENT_PACKAGE_SET (xml)</option>
703 <option value="runinfo-xml">SraRunInfo (xml)</option>
704 <option value="uilist-text">Unique Identifier List (text)</option>
705 <option value="uilist-xml">Unique Identifier List (xml)</option>
706 </param>
707 </when>
708 <when value="structure">
709 <param name="output_format" type="select" label="Output Format">
710 <option value="docsum-json">Document Summary (json)</option>
711 <option value="docsum-xml">Document Summary (xml)</option>
712 <option value="full-text">Full Document (text)</option>
713 <option value="full-xml">Full Document (xml)</option>
714 <option value="mmdb-asn.1">Ncbi-mime-asn1 strucseq (asn.1)</option>
715 <option value="native-text">MMDB Report (text)</option>
716 <option value="native-xml">RecordSet (xml)</option>
717 <option value="uilist-text">Unique Identifier List (text)</option>
718 <option value="uilist-xml">Unique Identifier List (xml)</option>
719 </param>
720 </when>
721 <when value="taxonomy">
722 <param name="output_format" type="select" label="Output Format">
723 <option value="docsum-json">Document Summary (json)</option>
724 <option value="docsum-xml">Document Summary (xml)</option>
725 <option value="full-text">Full Document (text)</option>
726 <option value="full-xml">Full Document (xml)</option>
727 <option value="native-text">Taxonomy List (text)</option>
728 <option value="native-xml">TaxaSet (xml)</option>
729 <option value="uilist-text">Unique Identifier List (text)</option>
730 <option value="uilist-xml">Unique Identifier List (xml)</option>
731 </param>
732 </when>
733 <when value="unigene">
734 <param name="output_format" type="select" label="Output Format">
735 <option value="docsum-json">Document Summary (json)</option>
736 <option value="docsum-xml">Document Summary (xml)</option>
737 <option value="full-text">Full Document (text)</option>
738 <option value="full-xml">Full Document (xml)</option>
739 <option value="uilist-text">Unique Identifier List (text)</option>
740 <option value="uilist-xml">Unique Identifier List (xml)</option>
741 </param>
742 </when>
743 </conditional>
744 </xml>
745
746 <xml name="efetch_formats">
747 <change_format>
748 <when input="output_format" value="fasta_cds_na-fasta" format="fasta"/>
749 <when input="output_format" value="ipg-xml" format="xml"/>
750 <when input="output_format" value="gbc-xml" format="xml"/>
751 <when input="output_format" value="medline-text" format="text"/>
752 <when input="output_format" value="native-None" format="text"/>
753 <when input="output_format" value="mmdb-asn.1" format="asn1"/>
754 <when input="output_format" value="seqid-asn.1" format="asn1"/>
755 <when input="output_format" value="acc-text" format="text"/>
756 <when input="output_format" value="summary-text" format="text"/>
757 <when input="output_format" value="gene_fasta-fasta" format="fasta"/>
758 <when input="output_format" value="native-text" format="text"/>
759 <when input="output_format" value="gbwithparts-text" format="text"/>
760 <when input="output_format" value="gpc-xml" format="xml"/>
761 <when input="output_format" value="fasta_cds_aa-fasta" format="fasta"/>
762 <when input="output_format" value="gp-text" format="text"/>
763 <when input="output_format" value="gss-text" format="text"/>
764 <when input="output_format" value="ipg-text" format="text"/>
765 <when input="output_format" value="uilist-xml" format="xml"/>
766 <when input="output_format" value="docsum-xml" format="xml"/>
767 <when input="output_format" value="rsr-tabular" format="tabular"/>
768 <when input="output_format" value="uilist-text" format="text"/>
769 <when input="output_format" value="gb-text" format="text"/>
770 <when input="output_format" value="chr-text" format="text"/>
771 <when input="output_format" value="alignmentscores-text" format="text"/>
772 <when input="output_format" value="native-asn.1" format="asn1"/>
773 <when input="output_format" value="gp-xml" format="xml"/>
774 <when input="output_format" value="tabular-tabular" format="tabular"/>
775 <when input="output_format" value="ssexemplar-text" format="text"/>
776 <when input="output_format" value="docsum-json" format="json"/>
777 <when input="output_format" value="fasta-xml" format="xml"/>
778 <when input="output_format" value="runinfo-xml" format="xml"/>
779 <when input="output_format" value="flt-text" format="text"/>
780 <when input="output_format" value="fasta-fasta" format="fasta"/>
781 <when input="output_format" value="full-text" format="text"/>
782 <when input="output_format" value="gb-xml" format="xml"/>
783 <when input="output_format" value="abstract-xml" format="xml"/>
784 <when input="output_format" value="full-xml" format="xml"/>
785 <when input="output_format" value="ft-text" format="text"/>
786 <when input="output_format" value="homologene-text" format="text"/>
787 <when input="output_format" value="est-xml" format="xml"/>
788 <when input="output_format" value="gene_table-xml" format="xml"/>
789 <when input="output_format" value="docset-text" format="text"/>
790 <when input="output_format" value="native-xml" format="xml"/>
791 </change_format>
792 </xml>
793 <token name="@LIST_OR_HIST@">
794 #if $query_source.qss == "history":
795 --history_file $query_source.history_file
796 #else if $query_source.qss == "id_file":
797 --id_list $query_source.id_file
798 #else if $query_source.qss == "id_list":
799 --id $query_source.id_list
800 #end if
801 </token>
802 <xml name="list_or_hist">
803 <conditional name="query_source">
804 <param name="qss" type="select" label="Select source for IDs">
805 <option value="history">NCBI WebEnv History</option>
806 <option value="id_file">File containing IDs (one per line)</option>
807 <option value="id_list">Direct Entry</option>
808 </param>
809 <when value="history">
810 <param label="History File" name="history_file" type="data" format="json"/>
811 </when>
812 <when value="id_file">
813 <param label="ID List" name="id_file" type="data" format="text,tabular"/>
814 </when>
815 <when value="id_list">
816 <param label="ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
817 </when>
818 </conditional>
819 </xml>
820 <xml name="history_out">
821 <data format="json" name="history" label="NCBI Entrez WebEnv History">
822 <yield/>
823 </data>
824 </xml>
825 <xml name="citations">
826 <citations>
827 <citation type="bibtex">@Book{ncbiEutils,
828 author = {Eric Sayers},
829 title = {Entrez Programming Utilities Help},
830 year = {2010},
831 publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
832 note = {http://ww.ncbi.nlm.nih.gov/books/NBK25500/}
833 }</citation>
834 </citations>
835 </xml>
836 <xml name="requirements">
837 <requirements>
838 <requirement type="package" version="2.7">python</requirement>
839 <requirement type="package" version="1.66">biopython</requirement>
840 </requirements>
841 </xml>
842 <xml name="linkname">
843 <param name="linkname" type="select" label="To NCBI Database">
844 <!-- TODO: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html -->
845 </param>
846 </xml>
847 </macros>