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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1f7b04db717bd82f93519fdc3f34f589bb671e48
author iuc
date Mon, 29 Jul 2024 07:07:05 +0000
parents 95c765cd38fc
children
comparison
equal deleted inserted replaced
1:582174a06db0 2:30d6deb77b2b
1 <tool id="ncbi_entrez_direct_esearch" name="NCBI ESearch" version="@TOOL_VERSION@"> 1 <tool id="ncbi_entrez_direct_esearch" name="NCBI ESearch" version="@TOOL_VERSION@">
2 <description>search NCBI Databases by text query</description> 2 <description>search NCBI Databases by text query</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>esearch -version</version_command> 7 <version_command>esearch -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @ECONTACT@ 9 @ECONTACT@
10 esearch 10 esearch
11 -db "${db.db}" 11 -db '${db.db}'
12 -sort "${db.sort}" 12 -sort '${db.sort}'
13 -query "${query}" 13 -query '${query}'
14 ${spell} 14 ${spell}
15 #if $date.constraint: 15 #if $date.constraint:
16 -datetype $date.datetype 16 -datetype $date.datetype
17 #if str( $date.days ): 17 #if str( $date.days ):
18 -days "${date.days}" 18 -days '${date.days}'
19 #end if 19 #end if
20 #if str( $date.mindate ): 20 #if str( $date.mindate ):
21 -mindate "${date.mindate}" 21 -mindate '${date.mindate}'
22 #end if 22 #end if
23 #if str( $date.maxdate ): 23 #if str( $date.maxdate ):
24 -maxdate "${date.maxdate}" 24 -maxdate '${date.maxdate}'
25 #end if 25 #end if
26 #end if 26 #end if
27 > '$output_xml' 27 > '$output_xml'
28 ]]> 28 ]]>
29 </command> 29 </command>
30 <inputs> 30 <inputs>
31 <conditional name="db"> 31 <conditional name="db">
32 <param name="db" type="select" label="Choose your DB" argument="-db"> 32 <param argument="-db" type="select" label="Choose your DB">
33 <option value="annotinfo">annotinfo</option> 33 <option value="annotinfo">annotinfo</option>
34 <option value="assembly">assembly</option> 34 <option value="assembly">assembly</option>
35 <option value="bioproject">bioproject</option> 35 <option value="bioproject">bioproject</option>
36 <option value="biosample">biosample</option> 36 <option value="biosample">biosample</option>
37 <option value="biosystems">biosystems</option> 37 <option value="biosystems">biosystems</option>
38 <option value="blastdbinfo">blastdbinfo</option> 38 <option value="blastdbinfo">blastdbinfo</option>
39 <option value="books">books</option> 39 <option value="books">books</option>
40 <option value="cdd">cdd</option> 40 <option value="cdd">cdd</option>
41 <option value="clinvar">clinvar</option> 41 <option value="clinvar">clinvar</option>
42 <option value="clone">clone</option> 42 <option value="clone">clone</option>
43 <option value="dbvar">dbvar</option> 43 <option value="dbvar">dbvar</option>
44 <option value="gap">gap</option> 44 <option value="gap">gap</option>
45 <option value="gapplus">gapplus</option> 45 <option value="gapplus">gapplus</option>
46 <option value="gds">gds</option> 46 <option value="gds">gds</option>
47 <option value="gencoll">gencoll</option> 47 <option value="gencoll">gencoll</option>
48 <option value="gene">gene</option> 48 <option value="gene">gene</option>
49 <option value="genome">genome</option> 49 <option value="genome">genome</option>
50 <option value="geoprofiles">geoprofiles</option> 50 <option value="geoprofiles">geoprofiles</option>
51 <option value="grasp">grasp</option> 51 <option value="grasp">grasp</option>
52 <option value="gtr">gtr</option> 52 <option value="gtr">gtr</option>
53 <option value="homologene">homologene</option> 53 <option value="homologene">homologene</option>
54 <option value="medgen">medgen</option> 54 <option value="medgen">medgen</option>
55 <option value="mesh">mesh</option> 55 <option value="mesh">mesh</option>
56 <option value="ncbisearch">ncbisearch</option> 56 <option value="ncbisearch">ncbisearch</option>
57 <option value="nlmcatalog">nlmcatalog</option> 57 <option value="nlmcatalog">nlmcatalog</option>
58 <option value="nuccore">nuccore</option> 58 <option value="nuccore">nuccore</option>
59 <option value="nucest">nucest</option> 59 <option value="nucest">nucest</option>
60 <option value="nucgss">nucgss</option> 60 <option value="nucgss">nucgss</option>
61 <option value="nucleotide">nucleotide</option> 61 <option value="nucleotide">nucleotide</option>
62 <option value="omim">omim</option> 62 <option value="omim">omim</option>
63 <option value="orgtrack">orgtrack</option> 63 <option value="orgtrack">orgtrack</option>
64 <option value="pcassay">pcassay</option> 64 <option value="pcassay">pcassay</option>
65 <option value="pccompound">pccompound</option> 65 <option value="pccompound">pccompound</option>
66 <option value="pcsubstance">pcsubstance</option> 66 <option value="pcsubstance">pcsubstance</option>
67 <option value="pmc">pmc</option> 67 <option value="pmc">pmc</option>
68 <option value="popset">popset</option> 68 <option value="popset">popset</option>
69 <option value="probe">probe</option> 69 <option value="probe">probe</option>
70 <option value="protein">protein</option> 70 <option value="protein">protein</option>
71 <option value="proteinclusters">proteinclusters</option> 71 <option value="proteinclusters">proteinclusters</option>
72 <option value="pubmed">pubmed</option> 72 <option value="pubmed">pubmed</option>
73 <option value="pubmedhealth">pubmedhealth</option> 73 <option value="pubmedhealth">pubmedhealth</option>
74 <option value="seqannot">seqannot</option> 74 <option value="seqannot">seqannot</option>
75 <option value="snp">snp</option> 75 <option value="snp">snp</option>
76 <option value="sra">sra</option> 76 <option value="sra">sra</option>
77 <option value="structure">structure</option> 77 <option value="structure">structure</option>
78 <option value="taxonomy">taxonomy</option> 78 <option value="taxonomy">taxonomy</option>
79 <option value="unigene">unigene</option> 79 <option value="unigene">unigene</option>
80 </param>
81 <when value="annotinfo">
82 <param argument="-sort" type="select" label="Sort results by">
83 <option value="Default Order">Default Order</option>
84 </param>
85 </when>
86 <when value="assembly">
87 <param argument="-sort" type="select" label="Sort results by">
88 <option value="Default Order">Default Order</option>
89 </param>
90 </when>
91 <when value="bioproject">
92 <param argument="-sort" type="select" label="Sort results by">
93 <option value="Default Order">Default Order</option>
94 </param>
95 </when>
96 <when value="biosample">
97 <param argument="-sort" type="select" label="Sort results by">
98 <option value="Default Order">Default Order</option>
99 </param>
100 </when>
101 <when value="biosystems">
102 <param argument="-sort" type="select" label="Sort results by">
103 <option value="Default Order">Default Order</option>
104 </param>
105 </when>
106 <when value="blastdbinfo">
107 <param argument="-sort" type="select" label="Sort results by">
108 <option value="Default Order">Default Order</option>
109 </param>
110 </when>
111 <when value="books">
112 <param argument="-sort" type="select" label="Sort results by">
113 <option value="Default Order">Default Order</option>
114 </param>
115 </when>
116 <when value="cdd">
117 <param argument="-sort" type="select" label="Sort results by">
118 <option value="Default Order">Default Order</option>
119 </param>
120 </when>
121 <when value="clinvar">
122 <param argument="-sort" type="select" label="Sort results by">
123 <option value="Default Order">Default Order</option>
124 </param>
125 </when>
126 <when value="clone">
127 <param argument="-sort" type="select" label="Sort results by">
128 <option value="Default Order">Default Order</option>
129 </param>
130 </when>
131 <when value="dbvar">
132 <param argument="-sort" type="select" label="Sort results by">
133 <option value="Default Order">Default Order</option>
134 </param>
135 </when>
136 <when value="gap">
137 <param argument="-sort" type="select" label="Sort results by">
138 <option value="Default Order">Default Order</option>
139 </param>
140 </when>
141 <when value="gapplus">
142 <param argument="-sort" type="select" label="Sort results by">
143 <option value="Default Order">Default Order</option>
144 </param>
145 </when>
146 <when value="gds">
147 <param argument="-sort" type="select" label="Sort results by">
148 <option value="Default Order">Default Order</option>
149 </param>
150 </when>
151 <when value="gencoll">
152 <param argument="-sort" type="select" label="Sort results by">
153 <option value="Default Order">Default Order</option>
154 </param>
155 </when>
156 <when value="gene">
157 <param argument="-sort" type="select" label="Sort results by">
158 <option value="Default Order">Default Order</option>
159 </param>
160 </when>
161 <when value="genome">
162 <param argument="-sort" type="select" label="Sort results by">
163 <option value="Default Order">Default Order</option>
164 </param>
165 </when>
166 <when value="geoprofiles">
167 <param argument="-sort" type="select" label="Sort results by">
168 <option value="Default Order">Default Order</option>
169 </param>
170 </when>
171 <when value="grasp">
172 <param argument="-sort" type="select" label="Sort results by">
173 <option value="Default Order">Default Order</option>
174 </param>
175 </when>
176 <when value="gtr">
177 <param argument="-sort" type="select" label="Sort results by">
178 <option value="Default Order">Default Order</option>
179 </param>
180 </when>
181 <when value="homologene">
182 <param argument="-sort" type="select" label="Sort results by">
183 <option value="Default Order">Default Order</option>
184 </param>
185 </when>
186 <when value="medgen">
187 <param argument="-sort" type="select" label="Sort results by">
188 <option value="Default Order">Default Order</option>
189 </param>
190 </when>
191 <when value="mesh">
192 <param argument="-sort" type="select" label="Sort results by">
193 <option value="Default Order">Default Order</option>
194 </param>
195 </when>
196 <when value="ncbisearch">
197 <param argument="-sort" type="select" label="Sort results by">
198 <option value="Default Order">Default Order</option>
199 </param>
200 </when>
201 <when value="nlmcatalog">
202 <param argument="-sort" type="select" label="Sort results by">
203 <option value="Default Order">Default Order</option>
204 </param>
205 </when>
206 <when value="nuccore">
207 <param argument="-sort" type="select" label="Sort results by">
208 <option value="Default Order">Default Order</option>
209 </param>
210 </when>
211 <when value="nucest">
212 <param argument="-sort" type="select" label="Sort results by">
213 <option value="Default Order">Default Order</option>
214 </param>
215 </when>
216 <when value="nucgss">
217 <param argument="-sort" type="select" label="Sort results by">
218 <option value="Default Order">Default Order</option>
219 </param>
220 </when>
221 <when value="nucleotide">
222 <param argument="-sort" type="select" label="Sort results by">
223 <option value="Default Order">Default Order</option>
224 </param>
225 </when>
226 <when value="omim">
227 <param argument="-sort" type="select" label="Sort results by">
228 <option value="Default Order">Default Order</option>
229 </param>
230 </when>
231 <when value="orgtrack">
232 <param argument="-sort" type="select" label="Sort results by">
233 <option value="Default Order">Default Order</option>
234 </param>
235 </when>
236 <when value="pcassay">
237 <param argument="-sort" type="select" label="Sort results by">
238 <option value="Default Order">Default Order</option>
239 </param>
240 </when>
241 <when value="pccompound">
242 <param argument="-sort" type="select" label="Sort results by">
243 <option value="Default Order">Default Order</option>
244 </param>
245 </when>
246 <when value="pcsubstance">
247 <param argument="-sort" type="select" label="Sort results by">
248 <option value="Default Order">Default Order</option>
249 </param>
250 </when>
251 <when value="pmc">
252 <param argument="-sort" type="select" label="Sort results by">
253 <option value="Default Order">Default Order</option>
254 </param>
255 </when>
256 <when value="popset">
257 <param argument="-sort" type="select" label="Sort results by">
258 <option value="Default Order">Default Order</option>
259 </param>
260 </when>
261 <when value="probe">
262 <param argument="-sort" type="select" label="Sort results by">
263 <option value="Default Order">Default Order</option>
264 </param>
265 </when>
266 <when value="protein">
267 <param argument="-sort" type="select" label="Sort results by">
268 <option value="Default Order">Default Order</option>
269 </param>
270 </when>
271 <when value="proteinclusters">
272 <param argument="-sort" type="select" label="Sort results by">
273 <option value="Default Order">Default Order</option>
274 </param>
275 </when>
276 <when value="pubmed">
277 <param argument="-sort" type="select" label="Sort results by">
278 <option value="Default Order">Default Order</option>
279 </param>
280 </when>
281 <when value="pubmedhealth">
282 <param argument="-sort" type="select" label="Sort results by">
283 <option value="Default Order">Default Order</option>
284 </param>
285 </when>
286 <when value="seqannot">
287 <param argument="-sort" type="select" label="Sort results by">
288 <option value="Default Order">Default Order</option>
289 </param>
290 </when>
291 <when value="snp">
292 <param argument="-sort" type="select" label="Sort results by">
293 <option value="Default Order">Default Order</option>
294 </param>
295 </when>
296 <when value="sra">
297 <param argument="-sort" type="select" label="Sort results by">
298 <option value="Default Order">Default Order</option>
299 </param>
300 </when>
301 <when value="structure">
302 <param argument="-sort" type="select" label="Sort results by">
303 <option value="Default Order">Default Order</option>
304 </param>
305 </when>
306 <when value="taxonomy">
307 <param argument="-sort" type="select" label="Sort results by">
308 <option value="Default Order">Default Order</option>
309 </param>
310 </when>
311 <when value="unigene">
312 <param argument="-sort" type="select" label="Sort results by">
313 <option value="Default Order">Default Order</option>
314 </param>
315 </when>
316 </conditional>
317 <param argument="-query" type="text" label="Search Term">
318 <sanitizer>
319 <valid>
320 <add value="'"/>
321 <add value="["/>
322 <add value="]"/>
323 </valid>
324 </sanitizer>
80 </param> 325 </param>
81 <when value="annotinfo"> 326 <param argument="-spell" type="boolean" truevalue="-spell" falsevalue="" checked="false" label="Correct misspellings in query"/>
82 <param name="sort" type="select" label="Sort results by" argument="-sort"> 327 <conditional name="date">
83 <option value="Default Order">Default Order</option> 328 <param name="constraint" type="select" label="Filter By Date">
329 <option value="True">Filter by date</option>
330 <option value="False">Don't filter</option>
84 </param> 331 </param>
85 </when> 332 <when value="True">
86 <when value="assembly"> 333 <param name="datetype" type="select" label="Date type">
87 <param name="sort" type="select" label="Sort results by" argument="-sort"> 334 <option value="PDAT">Publish Date</option>
88 <option value="Default Order">Default Order</option> 335 <option value="EDAT">Entrez Date</option>
89 </param> 336 <option value="MDAT">Modification Date</option>
90 </when> 337 </param>
91 <when value="bioproject"> 338 <param name="days" type="integer" min="1" value="" optional="True" label="Number of days in the past"/>
92 <param name="sort" type="select" label="Sort results by" argument="-sort"> 339 <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD"/>
93 <option value="Default Order">Default Order</option> 340 <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD"/>
94 </param> 341 </when>
95 </when> 342 <when value="False"/>
96 <when value="biosample"> 343 </conditional>
97 <param name="sort" type="select" label="Sort results by" argument="-sort"> 344 </inputs>
98 <option value="Default Order">Default Order</option> 345 <outputs>
99 </param> 346 <data format="xml" name="output_xml" label="ESearch Results for $query"/>
100 </when> 347 </outputs>
101 <when value="biosystems"> 348 <tests>
102 <param name="sort" type="select" label="Sort results by" argument="-sort"> 349 <test>
103 <option value="Default Order">Default Order</option> 350 <param name="db" value="sra"/>
104 </param> 351 <param name="query" value="SRP000007"/>
105 </when> 352 <output name="output_xml">
106 <when value="blastdbinfo"> 353 <assert_contents>
107 <param name="sort" type="select" label="Sort results by" argument="-sort"> 354 <has_text_matching expression="ENTREZ_DIRECT"/>
108 <option value="Default Order">Default Order</option> 355 <has_text_matching expression="sra"/>
109 </param> 356 <has_text_matching expression="WebEnv"/>
110 </when> 357 <has_text_matching expression="QueryKey"/>
111 <when value="books"> 358 <has_text_matching expression="Count"/>
112 <param name="sort" type="select" label="Sort results by" argument="-sort"> 359 <has_text_matching expression="Step"/>
113 <option value="Default Order">Default Order</option> 360 <has_text_matching expression="WebEnv"/>
114 </param> 361 </assert_contents>
115 </when> 362 </output>
116 <when value="cdd"> 363 </test>
117 <param name="sort" type="select" label="Sort results by" argument="-sort"> 364 </tests>
118 <option value="Default Order">Default Order</option> 365 <help><![CDATA[
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 366 NCBI Entrez ESearch
364 =================== 367 ===================
365 368
366 Responds to a text query with the list of matching UIDs in a given database 369 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 370 (for later use in ESummary, EFetch or ELink), along with the term translations
415 | Term | 70000:90000[molecular weight] | 418 | Term | 70000:90000[molecular weight] |
416 +----------------------+--------------------------------------+ 419 +----------------------+--------------------------------------+
417 420
418 @DISCLAIMER@ 421 @DISCLAIMER@
419 ]]></help> 422 ]]></help>
420 <expand macro="citations"/> 423 <expand macro="citations"/>
421 </tool> 424 </tool>