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comparison esearch.xml @ 0:b6ffd64c448e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
author iuc
date Tue, 22 Mar 2022 22:30:57 +0000
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children f6046ed1f915
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-1:000000000000 0:b6ffd64c448e
1 <tool id="ncbi_entrez_direct_esearch" name="NCBI ESearch" version="@TOOL_VERSION@">
2 <description>search NCBI Databases by text query</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>esearch -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[
9 @ECONTACT@
10 esearch
11 -db "${db.db}"
12 -sort "${db.sort}"
13 -query "${query}"
14 ${spell}
15 #if $date.constraint:
16 -datetype $date.datetype
17 #if str( $date.days ):
18 -days "${date.days}"
19 #end if
20 #if str( $date.mindate ):
21 -mindate "${date.mindate}"
22 #end if
23 #if str( $date.maxdate ):
24 -maxdate "${date.maxdate}"
25 #end if
26 #end if
27 > '$output_xml'
28 ]]>
29 </command>
30 <inputs>
31 <conditional name="db">
32 <param name="db" type="select" label="Choose your DB" argument="-db">
33 <option value="annotinfo">annotinfo</option>
34 <option value="assembly">assembly</option>
35 <option value="bioproject">bioproject</option>
36 <option value="biosample">biosample</option>
37 <option value="biosystems">biosystems</option>
38 <option value="blastdbinfo">blastdbinfo</option>
39 <option value="books">books</option>
40 <option value="cdd">cdd</option>
41 <option value="clinvar">clinvar</option>
42 <option value="clone">clone</option>
43 <option value="dbvar">dbvar</option>
44 <option value="gap">gap</option>
45 <option value="gapplus">gapplus</option>
46 <option value="gds">gds</option>
47 <option value="gencoll">gencoll</option>
48 <option value="gene">gene</option>
49 <option value="genome">genome</option>
50 <option value="geoprofiles">geoprofiles</option>
51 <option value="grasp">grasp</option>
52 <option value="gtr">gtr</option>
53 <option value="homologene">homologene</option>
54 <option value="medgen">medgen</option>
55 <option value="mesh">mesh</option>
56 <option value="ncbisearch">ncbisearch</option>
57 <option value="nlmcatalog">nlmcatalog</option>
58 <option value="nuccore">nuccore</option>
59 <option value="nucest">nucest</option>
60 <option value="nucgss">nucgss</option>
61 <option value="nucleotide">nucleotide</option>
62 <option value="omim">omim</option>
63 <option value="orgtrack">orgtrack</option>
64 <option value="pcassay">pcassay</option>
65 <option value="pccompound">pccompound</option>
66 <option value="pcsubstance">pcsubstance</option>
67 <option value="pmc">pmc</option>
68 <option value="popset">popset</option>
69 <option value="probe">probe</option>
70 <option value="protein">protein</option>
71 <option value="proteinclusters">proteinclusters</option>
72 <option value="pubmed">pubmed</option>
73 <option value="pubmedhealth">pubmedhealth</option>
74 <option value="seqannot">seqannot</option>
75 <option value="snp">snp</option>
76 <option value="sra">sra</option>
77 <option value="structure">structure</option>
78 <option value="taxonomy">taxonomy</option>
79 <option value="unigene">unigene</option>
80 </param>
81 <when value="annotinfo">
82 <param name="sort" type="select" label="Sort results by" argument="-sort">
83 <option value="Default Order">Default Order</option>
84 </param>
85 </when>
86 <when value="assembly">
87 <param name="sort" type="select" label="Sort results by" argument="-sort">
88 <option value="Default Order">Default Order</option>
89 </param>
90 </when>
91 <when value="bioproject">
92 <param name="sort" type="select" label="Sort results by" argument="-sort">
93 <option value="Default Order">Default Order</option>
94 </param>
95 </when>
96 <when value="biosample">
97 <param name="sort" type="select" label="Sort results by" argument="-sort">
98 <option value="Default Order">Default Order</option>
99 </param>
100 </when>
101 <when value="biosystems">
102 <param name="sort" type="select" label="Sort results by" argument="-sort">
103 <option value="Default Order">Default Order</option>
104 </param>
105 </when>
106 <when value="blastdbinfo">
107 <param name="sort" type="select" label="Sort results by" argument="-sort">
108 <option value="Default Order">Default Order</option>
109 </param>
110 </when>
111 <when value="books">
112 <param name="sort" type="select" label="Sort results by" argument="-sort">
113 <option value="Default Order">Default Order</option>
114 </param>
115 </when>
116 <when value="cdd">
117 <param name="sort" type="select" label="Sort results by" argument="-sort">
118 <option value="Default Order">Default Order</option>
119 </param>
120 </when>
121 <when value="clinvar">
122 <param name="sort" type="select" label="Sort results by" argument="-sort">
123 <option value="Default Order">Default Order</option>
124 </param>
125 </when>
126 <when value="clone">
127 <param name="sort" type="select" label="Sort results by" argument="-sort">
128 <option value="Default Order">Default Order</option>
129 </param>
130 </when>
131 <when value="dbvar">
132 <param name="sort" type="select" label="Sort results by" argument="-sort">
133 <option value="Default Order">Default Order</option>
134 </param>
135 </when>
136 <when value="gap">
137 <param name="sort" type="select" label="Sort results by" argument="-sort">
138 <option value="Default Order">Default Order</option>
139 </param>
140 </when>
141 <when value="gapplus">
142 <param name="sort" type="select" label="Sort results by" argument="-sort">
143 <option value="Default Order">Default Order</option>
144 </param>
145 </when>
146 <when value="gds">
147 <param name="sort" type="select" label="Sort results by" argument="-sort">
148 <option value="Default Order">Default Order</option>
149 </param>
150 </when>
151 <when value="gencoll">
152 <param name="sort" type="select" label="Sort results by" argument="-sort">
153 <option value="Default Order">Default Order</option>
154 </param>
155 </when>
156 <when value="gene">
157 <param name="sort" type="select" label="Sort results by" argument="-sort">
158 <option value="Default Order">Default Order</option>
159 </param>
160 </when>
161 <when value="genome">
162 <param name="sort" type="select" label="Sort results by" argument="-sort">
163 <option value="Default Order">Default Order</option>
164 </param>
165 </when>
166 <when value="geoprofiles">
167 <param name="sort" type="select" label="Sort results by" argument="-sort">
168 <option value="Default Order">Default Order</option>
169 </param>
170 </when>
171 <when value="grasp">
172 <param name="sort" type="select" label="Sort results by" argument="-sort">
173 <option value="Default Order">Default Order</option>
174 </param>
175 </when>
176 <when value="gtr">
177 <param name="sort" type="select" label="Sort results by" argument="-sort">
178 <option value="Default Order">Default Order</option>
179 </param>
180 </when>
181 <when value="homologene">
182 <param name="sort" type="select" label="Sort results by" argument="-sort">
183 <option value="Default Order">Default Order</option>
184 </param>
185 </when>
186 <when value="medgen">
187 <param name="sort" type="select" label="Sort results by" argument="-sort">
188 <option value="Default Order">Default Order</option>
189 </param>
190 </when>
191 <when value="mesh">
192 <param name="sort" type="select" label="Sort results by" argument="-sort">
193 <option value="Default Order">Default Order</option>
194 </param>
195 </when>
196 <when value="ncbisearch">
197 <param name="sort" type="select" label="Sort results by" argument="-sort">
198 <option value="Default Order">Default Order</option>
199 </param>
200 </when>
201 <when value="nlmcatalog">
202 <param name="sort" type="select" label="Sort results by" argument="-sort">
203 <option value="Default Order">Default Order</option>
204 </param>
205 </when>
206 <when value="nuccore">
207 <param name="sort" type="select" label="Sort results by" argument="-sort">
208 <option value="Default Order">Default Order</option>
209 </param>
210 </when>
211 <when value="nucest">
212 <param name="sort" type="select" label="Sort results by" argument="-sort">
213 <option value="Default Order">Default Order</option>
214 </param>
215 </when>
216 <when value="nucgss">
217 <param name="sort" type="select" label="Sort results by" argument="-sort">
218 <option value="Default Order">Default Order</option>
219 </param>
220 </when>
221 <when value="nucleotide">
222 <param name="sort" type="select" label="Sort results by" argument="-sort">
223 <option value="Default Order">Default Order</option>
224 </param>
225 </when>
226 <when value="omim">
227 <param name="sort" type="select" label="Sort results by" argument="-sort">
228 <option value="Default Order">Default Order</option>
229 </param>
230 </when>
231 <when value="orgtrack">
232 <param name="sort" type="select" label="Sort results by" argument="-sort">
233 <option value="Default Order">Default Order</option>
234 </param>
235 </when>
236 <when value="pcassay">
237 <param name="sort" type="select" label="Sort results by" argument="-sort">
238 <option value="Default Order">Default Order</option>
239 </param>
240 </when>
241 <when value="pccompound">
242 <param name="sort" type="select" label="Sort results by" argument="-sort">
243 <option value="Default Order">Default Order</option>
244 </param>
245 </when>
246 <when value="pcsubstance">
247 <param name="sort" type="select" label="Sort results by" argument="-sort">
248 <option value="Default Order">Default Order</option>
249 </param>
250 </when>
251 <when value="pmc">
252 <param name="sort" type="select" label="Sort results by" argument="-sort">
253 <option value="Default Order">Default Order</option>
254 </param>
255 </when>
256 <when value="popset">
257 <param name="sort" type="select" label="Sort results by" argument="-sort">
258 <option value="Default Order">Default Order</option>
259 </param>
260 </when>
261 <when value="probe">
262 <param name="sort" type="select" label="Sort results by" argument="-sort">
263 <option value="Default Order">Default Order</option>
264 </param>
265 </when>
266 <when value="protein">
267 <param name="sort" type="select" label="Sort results by" argument="-sort">
268 <option value="Default Order">Default Order</option>
269 </param>
270 </when>
271 <when value="proteinclusters">
272 <param name="sort" type="select" label="Sort results by" argument="-sort">
273 <option value="Default Order">Default Order</option>
274 </param>
275 </when>
276 <when value="pubmed">
277 <param name="sort" type="select" label="Sort results by" argument="-sort">
278 <option value="Default Order">Default Order</option>
279 </param>
280 </when>
281 <when value="pubmedhealth">
282 <param name="sort" type="select" label="Sort results by" argument="-sort">
283 <option value="Default Order">Default Order</option>
284 </param>
285 </when>
286 <when value="seqannot">
287 <param name="sort" type="select" label="Sort results by" argument="-sort">
288 <option value="Default Order">Default Order</option>
289 </param>
290 </when>
291 <when value="snp">
292 <param name="sort" type="select" label="Sort results by" argument="-sort">
293 <option value="Default Order">Default Order</option>
294 </param>
295 </when>
296 <when value="sra">
297 <param name="sort" type="select" label="Sort results by" argument="-sort">
298 <option value="Default Order">Default Order</option>
299 </param>
300 </when>
301 <when value="structure">
302 <param name="sort" type="select" label="Sort results by" argument="-sort">
303 <option value="Default Order">Default Order</option>
304 </param>
305 </when>
306 <when value="taxonomy">
307 <param name="sort" type="select" label="Sort results by" argument="-sort">
308 <option value="Default Order">Default Order</option>
309 </param>
310 </when>
311 <when value="unigene">
312 <param name="sort" type="select" label="Sort results by" argument="-sort">
313 <option value="Default Order">Default Order</option>
314 </param>
315 </when>
316 </conditional>
317 <param label="Search Term" name="query" type="text" argument="-query">
318 <sanitizer>
319 <valid>
320 <add value="'"/>
321 <add value="["/>
322 <add value="]"/>
323 </valid>
324 </sanitizer>
325 </param>
326 <param name="spell" label="Correct misspellings in query" type="boolean" truevalue="-spell" falsevalue="" checked="false"/>
327 <conditional name="date">
328 <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="constraint"/>
329 <when value="True">
330 <param label="Date type" name="datetype" type="select">
331 <option value="PDAT">Publish Date</option>
332 <option value="EDAT">Entrez Date</option>
333 <option value="MDAT">Modification Date</option>
334 </param>
335 <param label="Number of days in the past" name="days" value="" type="integer" min="1" optional="True"/>
336 <param label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="mindate" type="text"/>
337 <param label="Maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="maxdate" type="text"/>
338 </when>
339 <when value="False"/>
340 </conditional>
341 </inputs>
342 <outputs>
343 <data format="xml" name="output_xml" label="ESearch Results for $query"/>
344 </outputs>
345 <tests>
346 <test>
347 <param name="db" value="sra"/>
348 <param name="query" value="SRP000007"/>
349 <output name="output_xml">
350 <assert_contents>
351 <has_text_matching expression="ENTREZ_DIRECT" />
352 <has_text_matching expression="sra" />
353 <has_text_matching expression="WebEnv" />
354 <has_text_matching expression="QueryKey" />
355 <has_text_matching expression="Count" />
356 <has_text_matching expression="Step" />
357 <has_text_matching expression="WebEnv" />
358 </assert_contents>
359 </output>
360 </test>
361 </tests>
362 <help><![CDATA[
363 NCBI Entrez ESearch
364 ===================
365
366 Responds to a text query with the list of matching UIDs in a given database
367 (for later use in ESummary, EFetch or ELink), along with the term translations
368 of the query.
369
370 Example Queries
371 ---------------
372
373 Search in PubMed with the term cancer for abstracts that have an Entrez date
374 within the last 60 days:
375
376 +----------------------+-------------+
377 | Parameter | Value |
378 +======================+=============+
379 | NCBI Database to Use | PubMed |
380 +----------------------+-------------+
381 | Term | Cancer |
382 +----------------------+-------------+
383 | Datetype | Entrez Date |
384 +----------------------+-------------+
385 | In past N Days | 60 |
386 +----------------------+-------------+
387
388 Search PubMed Central for free full text articles containing the query stem cells:
389
390 +----------------------+--------------------------------------+
391 | Parameter | Value |
392 +======================+======================================+
393 | NCBI Database to Use | PubMedCentral |
394 +----------------------+--------------------------------------+
395 | Term | Stem Cells AND free fulltext[filter] |
396 +----------------------+--------------------------------------+
397
398 Search in Nucleotide for all tRNAs:
399
400 +----------------------+--------------------------------------+
401 | Parameter | Value |
402 +======================+======================================+
403 | NCBI Database to Use | Nucleotide |
404 +----------------------+--------------------------------------+
405 | Term | biomol trna[prop] |
406 +----------------------+--------------------------------------+
407
408 Search in Protein for a molecular weight range:
409
410 +----------------------+--------------------------------------+
411 | Parameter | Value |
412 +======================+======================================+
413 | NCBI Database to Use | Protein |
414 +----------------------+--------------------------------------+
415 | Term | 70000:90000[molecular weight] |
416 +----------------------+--------------------------------------+
417
418 @DISCLAIMER@
419 ]]></help>
420 <expand macro="citations"/>
421 </tool>