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comparison macros.xml @ 0:1b4ac594d02a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
author iuc
date Sat, 31 Oct 2015 12:44:54 -0400
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1 <?xml version="1.0"?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">1.0</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 <token name="@REFERENCES@"><![CDATA[
10 References
11 ==========
12
13 If you use this Galaxy tool in work leading to a scientific
14 publication, please cite the following papers:
15
16 ]]></token>
17 <token name="@DISCLAIMER@"><![CDATA[
18 Usage Guidelines and Requirements
19 =================================
20
21 Frequency, Timing, and Registration of E-utility URL Requests
22 -------------------------------------------------------------
23
24 In order not to overload the E-utility servers, NCBI recommends that users
25 limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time
26 during weekdays. Failure to comply with this policy may result in an IP address
27 being blocked from accessing NCBI.
28
29 Minimizing the Number of Requests
30 ---------------------------------
31
32 If a task requires searching for and/or downloading a large number of
33 records, it is much more efficient to use the Entrez History to upload
34 and/or retrieve these records in batches rather than using separate
35 requests for each record. Please refer to Application 3 in Chapter 3
36 for an example. Many thousands of IDs can be uploaded using a single
37 EPost request, and several hundred records can be downloaded using one
38 EFetch request.
39
40
41 Disclaimer and Copyright Issues
42 -------------------------------
43
44 In accordance with requirements of NCBI's E-Utilities, we must provide
45 the following disclaimer:
46
47 Please note that abstracts in PubMed may incorporate material that may
48 be protected by U.S. and foreign copyright laws. All persons
49 reproducing, redistributing, or making commercial use of this
50 information are expected to adhere to the terms and conditions asserted
51 by the copyright holder. Transmission or reproduction of protected
52 items beyond that allowed by fair use (PDF) as defined in the copyright
53 laws requires the written permission of the copyright owners. NLM
54 provides no legal advice concerning distribution of copyrighted
55 materials. Please consult your legal counsel. If you wish to do a large
56 data mining project on PubMed data, you can enter into a licensing
57 agreement and lease the data for free from NLM. For more information on
58 this please see `http://www.nlm.nih.gov/databases/leased.html <http://www.nlm.nih.gov/databases/leased.html>`__
59
60 The `full disclaimer <http://www.ncbi.nlm.nih.gov/About/disclaimer.html>`__ is available on
61 their website
62
63 Liability
64 ~~~~~~~~~
65
66 For documents and software available from this server, the
67 U.S. Government does not warrant or assume any legal liability or
68 responsibility for the accuracy, completeness, or usefulness of any
69 information, apparatus, product, or process disclosed.
70
71 Endorsement
72 ~~~~~~~~~~~
73
74 NCBI does not endorse or recommend any commercial
75 products, processes, or services. The views and opinions of authors
76 expressed on NCBI's Web sites do not necessarily state or reflect those
77 of the U.S. Government, and they may not be used for advertising or
78 product endorsement purposes.
79
80 External Links
81 ~~~~~~~~~~~~~~
82
83 Some NCBI Web pages may provide links to other Internet
84 sites for the convenience of users. NCBI is not responsible for the
85 availability or content of these external sites, nor does NCBI endorse,
86 warrant, or guarantee the products, services, or information described
87 or offered at these other Internet sites. Users cannot assume that the
88 external sites will abide by the same Privacy Policy to which NCBI
89 adheres. It is the responsibility of the user to examine the copyright
90 and licensing restrictions of linked pages and to secure all necessary
91 permissions.
92 ]]></token>
93 <xml name="stdio">
94 <stdio>
95 <!-- Anything other than zero is an error -->
96 <exit_code range="1:"/>
97 <exit_code range=":-1"/>
98 <!-- In case the return code has not been set propery check stderr too -->
99 <regex match="Error:"/>
100 <regex match="Exception:"/>
101 </stdio>
102 </xml>
103 <xml name="dbselect">
104 <param name="db_select" type="select" label="NCBI Database to Use">
105 <option value="assembly">Assembly</option>
106 <option value="bioproject">BioProject</option>
107 <option value="biosample">BioSample</option>
108 <option value="biosystems">Biosystems</option>
109 <option value="blastdbinfo">Blast Database Information</option>
110 <option value="books">Books</option>
111 <option value="cdd">Conserved Domains</option>
112 <option value="clinvar">Clinical Variants</option>
113 <option value="clone">CLone</option>
114 <option value="dbvar">dbVar</option>
115 <option value="epigenomics">Epigenomics</option>
116 <option value="gap">dbGaP</option>
117 <option value="gds">GEO Datasets</option>
118 <option value="gene">Gene</option>
119 <option value="genome">Genome</option>
120 <option value="geoprofiles">GEO Profiles</option>
121 <option value="gtr">Genetic Testing Registry</option>
122 <option value="homologene">HomoloGene</option>
123 <option value="journals">Journals</option>
124 <option value="medgen">MedGen</option>
125 <option value="mesh">MeSH</option>
126 <option value="ncbisearch">NCBI Web Site</option>
127 <option value="nlmcatalog">NLM Catalog</option>
128 <option value="nuccore">Nucleotide</option>
129 <option value="nucest">EST</option>
130 <option value="nucgss">GSS</option>
131 <option value="omim">OMIM</option>
132 <option value="pcassay">PubChem BioAssay</option>
133 <option value="pccompound">PubChem Compound</option>
134 <option value="pcsubstance">PubChem Substance</option>
135 <option value="pmc">PubMed Central</option>
136 <option value="popset">PopSet</option>
137 <option value="probe">Probe</option>
138 <option value="protein">Protein</option>
139 <option value="proteinclusters">Protein Clusters</option>
140 <option value="pubmed">PubMed</option>
141 <option value="pubmedhealth">PubMed Health</option>
142 <option value="snp">SNP</option>
143 <option value="sra">SRA</option>
144 <option value="structure">Structure</option>
145 <option value="taxonomy">Taxonomy</option>
146 <option value="toolkit">NCBI C++ Toolkit</option>
147 <option value="toolkitall">NCBI C++ Toolkit All</option>
148 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
149 <option value="unigene">UniGene</option>
150 </param>
151 </xml>
152 <xml name="db">
153 <conditional name="db">
154 <param name="db_select" type="select" label="NCBI Database to Use">
155 <option value="assembly">Assembly</option>
156 <option value="bioproject">BioProject</option>
157 <option value="biosample">BioSample</option>
158 <option value="biosystems">Biosystems</option>
159 <option value="blastdbinfo">Blast Database Information</option>
160 <option value="books">Books</option>
161 <option value="cdd">Conserved Domains</option>
162 <option value="clinvar">Clinical Variants</option>
163 <option value="clone">CLone</option>
164 <option value="dbvar">dbVar</option>
165 <option value="epigenomics">Epigenomics</option>
166 <option value="gap">dbGaP</option>
167 <option value="gds">GEO Datasets</option>
168 <option value="gene">Gene</option>
169 <option value="genome">Genome</option>
170 <option value="geoprofiles">GEO Profiles</option>
171 <option value="gtr">Genetic Testing Registry</option>
172 <option value="homologene">HomoloGene</option>
173 <option value="journals">Journals</option>
174 <option value="medgen">MedGen</option>
175 <option value="mesh">MeSH</option>
176 <option value="ncbisearch">NCBI Web Site</option>
177 <option value="nlmcatalog">NLM Catalog</option>
178 <option value="nuccore">Nucleotide</option>
179 <option value="nucest">EST</option>
180 <option value="nucgss">GSS</option>
181 <option value="omim">OMIM</option>
182 <option value="pcassay">PubChem BioAssay</option>
183 <option value="pccompound">PubChem Compound</option>
184 <option value="pcsubstance">PubChem Substance</option>
185 <option value="pmc">PubMed Central</option>
186 <option value="popset">PopSet</option>
187 <option value="probe">Probe</option>
188 <option value="protein">Protein</option>
189 <option value="proteinclusters">Protein Clusters</option>
190 <option value="pubmed">PubMed</option>
191 <option value="pubmedhealth">PubMed Health</option>
192 <option value="snp">SNP</option>
193 <option value="sra">SRA</option>
194 <option value="structure">Structure</option>
195 <option value="taxonomy">Taxonomy</option>
196 <option value="toolkit">NCBI C++ Toolkit</option>
197 <option value="toolkitall">NCBI C++ Toolkit All</option>
198 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
199 <option value="unigene">UniGene</option>
200 </param>
201 <when value="assembly">
202 <param name="output_format" type="select" label="Output Format">
203 <option value="docsum-xml">Document summary</option>
204 <option value="uilist-xml">List of UIDs (XML)</option>
205 <option value="uilist-text">List of UIDs (plain text)</option>
206 </param>
207 </when>
208 <when value="bioproject">
209 <param name="output_format" type="select" label="Output Format">
210 <option value="docsum-xml">Document summary</option>
211 <option value="uilist-xml">List of UIDs (XML)</option>
212 <option value="uilist-text">List of UIDs (plain text)</option>
213 <option value="xml-xml">Full record</option>
214 </param>
215 </when>
216 <when value="biosample">
217 <param name="output_format" type="select" label="Output Format">
218 <option value="docsum-xml">Document summary</option>
219 <option value="uilist-xml">List of UIDs (XML)</option>
220 <option value="uilist-text">List of UIDs (plain text)</option>
221 <option value="full-xml">Full record (XML)</option>
222 <option value="full-text">Full record (plain text)</option>
223 </param>
224 </when>
225 <when value="biosystems">
226 <param name="output_format" type="select" label="Output Format">
227 <option value="docsum-xml">Document summary</option>
228 <option value="uilist-xml">List of UIDs (XML)</option>
229 <option value="uilist-text">List of UIDs (plain text)</option>
230 <option value="xml-xml">Full record</option>
231 </param>
232 </when>
233 <when value="blastdbinfo">
234 <param name="output_format" type="select" label="Output Format">
235 <option value="docsum-xml">Document summary</option>
236 <option value="uilist-xml">List of UIDs (XML)</option>
237 <option value="uilist-text">List of UIDs (plain text)</option>
238 </param>
239 </when>
240 <when value="books">
241 <param name="output_format" type="select" label="Output Format">
242 <option value="docsum-xml">Document summary</option>
243 <option value="uilist-xml">List of UIDs (XML)</option>
244 <option value="uilist-text">List of UIDs (plain text)</option>
245 </param>
246 </when>
247 <when value="cdd">
248 <param name="output_format" type="select" label="Output Format">
249 <option value="docsum-xml">Document summary</option>
250 <option value="uilist-xml">List of UIDs (XML)</option>
251 <option value="uilist-text">List of UIDs (plain text)</option>
252 </param>
253 </when>
254 <when value="clinvar">
255 <param name="output_format" type="select" label="Output Format">
256 <option value="docsum-xml">Document summary</option>
257 <option value="uilist-xml">List of UIDs (XML)</option>
258 <option value="uilist-text">List of UIDs (plain text)</option>
259 </param>
260 </when>
261 <when value="clone">
262 <param name="output_format" type="select" label="Output Format">
263 <option value="docsum-xml">Document summary</option>
264 <option value="uilist-xml">List of UIDs (XML)</option>
265 <option value="uilist-text">List of UIDs (plain text)</option>
266 </param>
267 </when>
268 <when value="dbvar">
269 <param name="output_format" type="select" label="Output Format">
270 <option value="docsum-xml">Document summary</option>
271 <option value="uilist-xml">List of UIDs (XML)</option>
272 <option value="uilist-text">List of UIDs (plain text)</option>
273 </param>
274 </when>
275 <when value="epigenomics">
276 <param name="output_format" type="select" label="Output Format">
277 <option value="docsum-xml">Document summary</option>
278 <option value="uilist-xml">List of UIDs (XML)</option>
279 <option value="uilist-text">List of UIDs (plain text)</option>
280 </param>
281 </when>
282 <when value="gap">
283 <param name="output_format" type="select" label="Output Format">
284 <option value="docsum-xml">Document summary</option>
285 <option value="uilist-xml">List of UIDs (XML)</option>
286 <option value="uilist-text">List of UIDs (plain text)</option>
287 </param>
288 </when>
289 <when value="gds">
290 <param name="output_format" type="select" label="Output Format">
291 <option value="docsum-xml">Document summary</option>
292 <option value="uilist-xml">List of UIDs (XML)</option>
293 <option value="uilist-text">List of UIDs (plain text)</option>
294 <option value="summary-text">Summary</option>
295 </param>
296 </when>
297 <when value="gene">
298 <param name="output_format" type="select" label="Output Format">
299 <option value="docsum-xml">Document summary</option>
300 <option value="uilist-xml">List of UIDs (XML)</option>
301 <option value="uilist-text">List of UIDs (plain text)</option>
302 <option value="null-asn.1">text (ASN.1)</option>
303 <option value="null-xml">XML</option>
304 <option value="gene_table-text">Gene table</option>
305 </param>
306 </when>
307 <when value="genome">
308 <param name="output_format" type="select" label="Output Format">
309 <option value="docsum-xml">Document summary</option>
310 <option value="uilist-xml">List of UIDs (XML)</option>
311 <option value="uilist-text">List of UIDs (plain text)</option>
312 </param>
313 </when>
314 <when value="geoprofiles">
315 <param name="output_format" type="select" label="Output Format">
316 <option value="docsum-xml">Document summary</option>
317 <option value="uilist-xml">List of UIDs (XML)</option>
318 <option value="uilist-text">List of UIDs (plain text)</option>
319 </param>
320 </when>
321 <when value="gtr">
322 <param name="output_format" type="select" label="Output Format">
323 <option value="docsum-xml">Document summary</option>
324 <option value="uilist-xml">List of UIDs (XML)</option>
325 <option value="uilist-text">List of UIDs (plain text)</option>
326 </param>
327 </when>
328 <when value="homologene">
329 <param name="output_format" type="select" label="Output Format">
330 <option value="docsum-xml">Document summary</option>
331 <option value="uilist-xml">List of UIDs (XML)</option>
332 <option value="uilist-text">List of UIDs (plain text)</option>
333 <option value="null-asn.1">text ASN.1</option>
334 <option value="null-xml">XML</option>
335 <option value="alignmentscores-text">Alignment scores</option>
336 <option value="fasta-text">FASTA</option>
337 <option value="homologene-text">HomoloGene</option>
338 </param>
339 </when>
340 <when value="journals">
341 <param name="output_format" type="select" label="Output Format">
342 <option value="docsum-xml">Document summary</option>
343 <option value="uilist-xml">List of UIDs (XML)</option>
344 <option value="uilist-text">List of UIDs (plain text)</option>
345 </param>
346 </when>
347 <when value="medgen">
348 <param name="output_format" type="select" label="Output Format">
349 <option value="docsum-xml">Document summary</option>
350 <option value="uilist-xml">List of UIDs (XML)</option>
351 <option value="uilist-text">List of UIDs (plain text)</option>
352 </param>
353 </when>
354 <when value="mesh">
355 <param name="output_format" type="select" label="Output Format">
356 <option value="docsum-xml">Document summary</option>
357 <option value="uilist-xml">List of UIDs (XML)</option>
358 <option value="uilist-text">List of UIDs (plain text)</option>
359 <option value="full-text">Full record</option>
360 </param>
361 </when>
362 <when value="ncbisearch">
363 <param name="output_format" type="select" label="Output Format">
364 <option value="docsum-xml">Document summary</option>
365 <option value="uilist-xml">List of UIDs (XML)</option>
366 <option value="uilist-text">List of UIDs (plain text)</option>
367 </param>
368 </when>
369 <when value="nlmcatalog">
370 <param name="output_format" type="select" label="Output Format">
371 <option value="docsum-xml">Document summary</option>
372 <option value="uilist-xml">List of UIDs (XML)</option>
373 <option value="uilist-text">List of UIDs (plain text)</option>
374 <option value="null-text">Full record</option>
375 <option value="null-xml">XML</option>
376 </param>
377 </when>
378 <when value="nuccore">
379 <param name="output_format" type="select" label="Output Format">
380 <option value="docsum-xml">Document summary</option>
381 <option value="uilist-xml">List of UIDs (XML)</option>
382 <option value="uilist-text">List of UIDs (plain text)</option>
383 <option value="null-text">text ASN.1</option>
384 <option value="null-asn.1">binary ASN.1</option>
385 <option value="native-xml">Full record in XML</option>
386 <option value="acc-text">Accession number(s)</option>
387 <option value="fasta-text">FASTA</option>
388 <option value="fasta-xml">TinySeq XML</option>
389 <option value="seqid-text">SeqID string</option>
390 <option value="gb-text">GenBank flat file</option>
391 <option value="gb-xml">GBSeq XML</option>
392 <option value="gbc-xml">INSDSeq XML</option>
393 <option value="ft-text">Feature table</option>
394 <option value="gbwithparts-text">GenBank flat file with full sequence (contigs)</option>
395 <option value="fasta_cds_na-text">CDS nucleotide FASTA</option>
396 <option value="fasta_cds_aa-text">CDS protein FASTA</option>
397 </param>
398 </when>
399 <when value="nucest">
400 <param name="output_format" type="select" label="Output Format">
401 <option value="docsum-xml">Document summary</option>
402 <option value="uilist-xml">List of UIDs (XML)</option>
403 <option value="uilist-text">List of UIDs (plain text)</option>
404 <option value="null-text">text ASN.1</option>
405 <option value="null-asn.1">binary ASN.1</option>
406 <option value="native-xml">Full record in XML</option>
407 <option value="acc-text">Accession number(s)</option>
408 <option value="fasta-text">FASTA</option>
409 <option value="fasta-xml">TinySeq XML</option>
410 <option value="seqid-text">SeqID string</option>
411 <option value="gb-text">GenBank flat file</option>
412 <option value="gb-xml">GBSeq XML</option>
413 <option value="gbc-xml">INSDSeq XML</option>
414 <option value="est-text">EST report</option>
415 </param>
416 </when>
417 <when value="nucgss">
418 <param name="output_format" type="select" label="Output Format">
419 <option value="docsum-xml">Document summary</option>
420 <option value="uilist-xml">List of UIDs (XML)</option>
421 <option value="uilist-text">List of UIDs (plain text)</option>
422 <option value="null-text">text ASN.1</option>
423 <option value="null-asn.1">binary ASN.1</option>
424 <option value="native-xml">Full record in XML</option>
425 <option value="acc-text">Accession number(s)</option>
426 <option value="fasta-text">FASTA</option>
427 <option value="fasta-xml">TinySeq XML</option>
428 <option value="seqid-text">SeqID string</option>
429 <option value="gb-text">GenBank flat file</option>
430 <option value="gb-xml">GBSeq XML</option>
431 <option value="gbc-xml">INSDSeq XML</option>
432 <option value="gss-text">GSS report</option>
433 </param>
434 </when>
435 <when value="omim">
436 <param name="output_format" type="select" label="Output Format">
437 <option value="docsum-xml">Document summary</option>
438 <option value="uilist-xml">List of UIDs (XML)</option>
439 <option value="uilist-text">List of UIDs (plain text)</option>
440 </param>
441 </when>
442 <when value="pcassay">
443 <param name="output_format" type="select" label="Output Format">
444 <option value="docsum-xml">Document summary</option>
445 <option value="uilist-xml">List of UIDs (XML)</option>
446 <option value="uilist-text">List of UIDs (plain text)</option>
447 </param>
448 </when>
449 <when value="pccompound">
450 <param name="output_format" type="select" label="Output Format">
451 <option value="docsum-xml">Document summary</option>
452 <option value="uilist-xml">List of UIDs (XML)</option>
453 <option value="uilist-text">List of UIDs (plain text)</option>
454 </param>
455 </when>
456 <when value="pcsubstance">
457 <param name="output_format" type="select" label="Output Format">
458 <option value="docsum-xml">Document summary</option>
459 <option value="uilist-xml">List of UIDs (XML)</option>
460 <option value="uilist-text">List of UIDs (plain text)</option>
461 </param>
462 </when>
463 <when value="pmc">
464 <param name="output_format" type="select" label="Output Format">
465 <option value="docsum-xml">Document summary</option>
466 <option value="uilist-xml">List of UIDs (XML)</option>
467 <option value="uilist-text">List of UIDs (plain text)</option>
468 <option value="null-xml">XML</option>
469 <option value="medline-text">MEDLINE</option>
470 </param>
471 </when>
472 <when value="popset">
473 <param name="output_format" type="select" label="Output Format">
474 <option value="docsum-xml">Document summary</option>
475 <option value="uilist-xml">List of UIDs (XML)</option>
476 <option value="uilist-text">List of UIDs (plain text)</option>
477 <option value="null-text">text ASN.1</option>
478 <option value="null-asn.1">binary ASN.1</option>
479 <option value="native-xml">Full record in XML</option>
480 <option value="acc-text">Accession number(s)</option>
481 <option value="fasta-text">FASTA</option>
482 <option value="fasta-xml">TinySeq XML</option>
483 <option value="seqid-text">SeqID string</option>
484 <option value="gb-text">GenBank flat file</option>
485 <option value="gb-xml">GBSeq XML</option>
486 <option value="gbc-xml">INSDSeq XML</option>
487 </param>
488 </when>
489 <when value="probe">
490 <param name="output_format" type="select" label="Output Format">
491 <option value="docsum-xml">Document summary</option>
492 <option value="uilist-xml">List of UIDs (XML)</option>
493 <option value="uilist-text">List of UIDs (plain text)</option>
494 </param>
495 </when>
496 <when value="protein">
497 <param name="output_format" type="select" label="Output Format">
498 <option value="docsum-xml">Document summary</option>
499 <option value="uilist-xml">List of UIDs (XML)</option>
500 <option value="uilist-text">List of UIDs (plain text)</option>
501 <option value="null-text">text ASN.1</option>
502 <option value="null-asn.1">binary ASN.1</option>
503 <option value="native-xml">Full record in XML</option>
504 <option value="acc-text">Accession number(s)</option>
505 <option value="fasta-text">FASTA</option>
506 <option value="fasta-xml">TinySeq XML</option>
507 <option value="seqid-text">SeqID string</option>
508 <option value="ft-text">Feature table</option>
509 <option value="gp-text">GenPept flat file</option>
510 <option value="gp-xml">GBSeq XML</option>
511 <option value="gpc-xml">INSDSeq XML</option>
512 <option value="ipg-xml">Identical Protein XML</option>
513 </param>
514 </when>
515 <when value="proteinclusters">
516 <param name="output_format" type="select" label="Output Format">
517 <option value="docsum-xml">Document summary</option>
518 <option value="uilist-xml">List of UIDs (XML)</option>
519 <option value="uilist-text">List of UIDs (plain text)</option>
520 </param>
521 </when>
522 <when value="pubmed">
523 <param name="output_format" type="select" label="Output Format">
524 <option value="docsum-xml">Document summary</option>
525 <option value="uilist-xml">List of UIDs (XML)</option>
526 <option value="uilist-text">List of UIDs (plain text)</option>
527 <option value="null-asn.1">text ASN.1</option>
528 <option value="null-xml">XML</option>
529 <option value="medline-text">MEDLINE</option>
530 <option value="uilist-text">PMID list</option>
531 <option value="abstract-text">Abstract</option>
532 </param>
533 </when>
534 <when value="pubmedhealth">
535 <param name="output_format" type="select" label="Output Format">
536 <option value="docsum-xml">Document summary</option>
537 <option value="uilist-xml">List of UIDs (XML)</option>
538 <option value="uilist-text">List of UIDs (plain text)</option>
539 </param>
540 </when>
541 <when value="snp">
542 <param name="output_format" type="select" label="Output Format">
543 <option value="docsum-xml">Document summary</option>
544 <option value="uilist-xml">List of UIDs (XML)</option>
545 <option value="uilist-text">List of UIDs (plain text)</option>
546 <option value="null-asn.1">text ASN.1</option>
547 <option value="null-xml">XML</option>
548 <option value="flt-text">Flat file</option>
549 <option value="fasta-text">FASTA</option>
550 <option value="rsr-text">RS Cluster report</option>
551 <option value="ssexemplar-text">SS Exemplar list</option>
552 <option value="chr-text">Chromosome report</option>
553 <option value="docset-text">Summary</option>
554 <option value="uilist-xml">UID list (XML)</option>
555 <option value="uilist-text">UID list (text)</option>
556 </param>
557 </when>
558 <when value="sra">
559 <param name="output_format" type="select" label="Output Format">
560 <option value="docsum-xml">Document summary</option>
561 <option value="uilist-xml">List of UIDs (XML)</option>
562 <option value="uilist-text">List of UIDs (plain text)</option>
563 <option value="full-xml">XML</option>
564 </param>
565 </when>
566 <when value="structure">
567 <param name="output_format" type="select" label="Output Format">
568 <option value="docsum-xml">Document summary</option>
569 <option value="uilist-xml">List of UIDs (XML)</option>
570 <option value="uilist-text">List of UIDs (plain text)</option>
571 </param>
572 </when>
573 <when value="taxonomy">
574 <param name="output_format" type="select" label="Output Format">
575 <option value="docsum-xml">Document summary</option>
576 <option value="uilist-xml">List of UIDs (XML)</option>
577 <option value="uilist-text">List of UIDs (plain text)</option>
578 <option value="null-xml">XML</option>
579 <option value="uilist-xml">TaxID list (XML)</option>
580 <option value="uilist-text">TaxID list (text)</option>
581 </param>
582 </when>
583 </conditional>
584 </xml>
585 <token name="@LIST_OR_HIST@">
586 #if $query_source.qss == "history":
587 --history_file $query_source.history_file
588 #else if $query_source.qss == "id_file":
589 --id_list $query_source.id_file
590 #else if $query_source.qss == "id_list":
591 --id $query_source.id_list
592 #end if
593 </token>
594 <xml name="list_or_hist">
595 <conditional name="query_source">
596 <param name="qss" type="select" label="Select source for IDs">
597 <option value="history">NCBI WebEnv History</option>
598 <option value="id_file">File containing IDs (one per line)</option>
599 <option value="id_list">Direct Entry</option>
600 </param>
601 <when value="history">
602 <param label="History File" name="history_file" type="data" format="ncbi_history"/>
603 </when>
604 <when value="id_file">
605 <param label="ID List" name="id_file" type="data" format="text,tabular"/>
606 </when>
607 <when value="id_list">
608 <param label="ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
609 </when>
610 </conditional>
611 </xml>
612 <xml name="history_out">
613 <data format="ncbi_history" name="history" label="NCBI Entrez WebEnv History">
614 <yield/>
615 </data>
616 </xml>
617 <xml name="citations">
618 <citations>
619 <citation type="bibtex">@Book{ncbiEutils,
620 author = {Eric Sayers},
621 title = {Entrez Programming Utilities Help},
622 year = {2010},
623 publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
624 note = {http://ww.ncbi.nlm.nih.gov/books/NBK25500/}
625 }</citation>
626 </citations>
627 </xml>
628 <xml name="db_select_to">
629 <param name="db_select_to" type="select" label="To NCBI Database">
630 <option value="assembly">Assembly</option>
631 <option value="bioproject">BioProject</option>
632 <option value="biosample">BioSample</option>
633 <option value="biosystems">Biosystems</option>
634 <option value="blastdbinfo">Blast Database Information</option>
635 <option value="books">Books</option>
636 <option value="cdd">Conserved Domains</option>
637 <option value="clinvar">Clinical Variants</option>
638 <option value="clone">CLone</option>
639 <option value="dbvar">dbVar</option>
640 <option value="epigenomics">Epigenomics</option>
641 <option value="gap">dbGaP</option>
642 <option value="gds">GEO Datasets</option>
643 <option value="gene">Gene</option>
644 <option value="genome">Genome</option>
645 <option value="geoprofiles">GEO Profiles</option>
646 <option value="gtr">Genetic Testing Registry</option>
647 <option value="homologene">HomoloGene</option>
648 <option value="journals">Journals</option>
649 <option value="medgen">MedGen</option>
650 <option value="mesh">MeSH</option>
651 <option value="ncbisearch">NCBI Web Site</option>
652 <option value="nlmcatalog">NLM Catalog</option>
653 <option value="nuccore">Nucleotide</option>
654 <option value="nucest">EST</option>
655 <option value="nucgss">GSS</option>
656 <option value="omim">OMIM</option>
657 <option value="pcassay">PubChem BioAssay</option>
658 <option value="pccompound">PubChem Compound</option>
659 <option value="pcsubstance">PubChem Substance</option>
660 <option value="pmc">PubMed Central</option>
661 <option value="popset">PopSet</option>
662 <option value="probe">Probe</option>
663 <option value="protein">Protein</option>
664 <option value="proteinclusters">Protein Clusters</option>
665 <option value="pubmed">PubMed</option>
666 <option value="pubmedhealth">PubMed Health</option>
667 <option value="snp">SNP</option>
668 <option value="sra">SRA</option>
669 <option value="structure">Structure</option>
670 <option value="taxonomy">Taxonomy</option>
671 <option value="toolkit">NCBI C++ Toolkit</option>
672 <option value="toolkitall">NCBI C++ Toolkit All</option>
673 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
674 <option value="unigene">UniGene</option>
675 </param>
676 </xml>
677 <xml name="requirements">
678 <requirements>
679 <requirement type="package" version="1.66">biopython</requirement>
680 </requirements>
681 </xml>
682 <xml name="linkname">
683 <param name="linkname" type="select" label="To NCBI Database">
684 <!-- TODO: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html -->
685 </param>
686 </xml>
687 </macros>