comparison search_macros.xml @ 0:c320e878909a draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
author iuc
date Tue, 29 Aug 2017 04:13:49 -0400
parents
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-1:000000000000 0:c320e878909a
1 <?xml version="1.0" ?>
2 <macros>
3 <xml name="analysis_fields">
4 <option value="analysis_accession">analysis_accession</option>
5 <option value="study_accession">study_accession</option>
6 <option value="secondary_study_accession">secondary_study_accession</option>
7 <option value="sample_accession">sample_accession</option>
8 <option value="secondary_sample_accession">secondary_sample_accession</option>
9 <option value="analysis_title">analysis_title</option>
10 <option value="analysis_type">analysis_type</option>
11 <option value="center_name">center_name</option>
12 <option value="first_public">first_public</option>
13 <option value="last_updated">last_updated</option>
14 <option value="study_title">study_title</option>
15 <option value="tax_id">tax_id</option>
16 <option value="scientific_name">scientific_name</option>
17 <option value="analysis_alias">analysis_alias</option>
18 <option value="study_alias">study_alias</option>
19 <option value="submitted_bytes">submitted_bytes</option>
20 <option value="submitted_md5">submitted_md5</option>
21 <option value="submitted_ftp">submitted_ftp</option>
22 <option value="submitted_aspera">submitted_aspera</option>
23 <option value="submitted_galaxy">submitted_galaxy</option>
24 <option value="sample_alias">sample_alias</option>
25 <option value="broker_name">broker_name</option>
26 </xml>
27 <xml name="display_options">
28 <option value="xml">Results are displayed in XML format. Supported by all ENA data classes.</option>
29 <option value="text">Results are displayed in text format. Supported only by assembled and annotated sequence data classes.</option>
30 <option value="fastq">Results are displayed in fastq format. Supported only by Trace data class.</option>
31 <option value="html">Results are displayed in HTML format. Supported by all ENA data classes. HTML is the default display format if no other display option has been specified.</option>
32 <option value="report">Results are displayed as a tab separated report</option>
33 <option value="fasta">Results are displayed in fasta format. Supported by assembled and annotated sequence and Trace data classes.</option>
34 </xml>
35 <xml name="when_display_options">
36 <when value="xml">
37 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
38 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
39 </when>
40 <when value="text">
41 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
42 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
43 </when>
44 <when value="fastq">
45 <param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/>
46 <param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/>
47 </when>
48 <when value="html">
49 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
50 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
51 </when>
52 <when value="report">
53 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
54 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
55 </when>
56 <when value="fasta">
57 <param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/>
58 <param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/>
59 </when>
60 </xml>
61 <xml name="run_fields">
62 <option value="study_accession">study_accession</option>
63 <option value="secondary_study_accession">secondary_study_accession</option>
64 <option value="sample_accession">sample_accession</option>
65 <option value="secondary_sample_accession">secondary_sample_accession</option>
66 <option value="experiment_accession">experiment_accession</option>
67 <option value="run_accession">run_accession</option>
68 <option value="submission_accession">submission_accession</option>
69 <option value="tax_id">tax_id</option>
70 <option value="scientific_name">scientific_name</option>
71 <option value="instrument_platform">instrument_platform</option>
72 <option value="instrument_model">instrument_model</option>
73 <option value="library_name">library_name</option>
74 <option value="nominal_length">nominal_length</option>
75 <option value="library_layout">library_layout</option>
76 <option value="library_strategy">library_strategy</option>
77 <option value="library_source">library_source</option>
78 <option value="library_selection">library_selection</option>
79 <option value="read_count">read_count</option>
80 <option value="base_count">base_count</option>
81 <option value="center_name">center_name</option>
82 <option value="first_public">first_public</option>
83 <option value="last_updated">last_updated</option>
84 <option value="experiment_title">experiment_title</option>
85 <option value="study_title">study_title</option>
86 <option value="study_alias">study_alias</option>
87 <option value="experiment_alias">experiment_alias</option>
88 <option value="run_alias">run_alias</option>
89 <option value="fastq_bytes">fastq_bytes</option>
90 <option value="fastq_md5">fastq_md5</option>
91 <option value="fastq_ftp">fastq_ftp</option>
92 <option value="fastq_aspera">fastq_aspera</option>
93 <option value="fastq_galaxy">fastq_galaxy</option>
94 <option value="submitted_bytes">submitted_bytes</option>
95 <option value="submitted_md5">submitted_md5</option>
96 <option value="submitted_ftp">submitted_ftp</option>
97 <option value="submitted_aspera">submitted_aspera</option>
98 <option value="submitted_galaxy">submitted_galaxy</option>
99 <option value="submitted_format">submitted_format</option>
100 <option value="sra_bytes">sra_bytes</option>
101 <option value="sra_md5">sra_md5</option>
102 <option value="sra_ftp">sra_ftp</option>
103 <option value="sra_aspera">sra_aspera</option>
104 <option value="sra_galaxy">sra_galaxy</option>
105 <option value="cram_index_ftp">cram_index_ftp</option>
106 <option value="cram_index_aspera">cram_index_aspera</option>
107 <option value="cram_index_galaxy">cram_index_galaxy</option>
108 <option value="sample_alias">sample_alias</option>
109 <option value="broker_name">broker_name</option>
110 </xml>
111 <xml name="taxonomy_results">
112 <option value="noncoding_release">Non-coding sequences (Release)</option>
113 <option value="sequence_release">Nucleotide Sequences (Release)</option>
114 <option value="study">Studies</option>
115 <option value="read_trace">Capillary Traces in Trace Archive</option>
116 <option value="coding_release">Protein-coding sequences (Release)</option>
117 <option value="sample">Samples</option>
118 <option value="read_run">Raw reads</option>
119 <option value="read_study">Raw reads (grouped by study)</option>
120 <option value="read_experiment">Raw reads (grouped by experiment)</option>
121 <option value="analysis">Nucleotide sequence analyses</option>
122 <option value="sequence_update">Nucleotide Sequences (Update)</option>
123 <option value="coding_update">Protein-coding sequences (Update)</option>
124 <option value="analysis_study">Nucleotide sequence analyses (grouped by study)</option>
125 <option value="noncoding_update">Non-coding sequences (Update)</option>
126 </xml>
127 <xml name="free_text_search">
128 <conditional name="res">
129 <param argument="--result" type="select" label="Result to return">
130 <option value="noncoding_release">Non-coding sequences (Release)</option>
131 <option value="assembly">Genome assemblies</option>
132 <option value="sequence_release">Nucleotide sequences (Release)</option>
133 <option value="wgs_set">Genome assembly contig set</option>
134 <option value="study">Studies</option>
135 <option value="taxon">Taxonomic classification</option>
136 <option value="coding_release">Protein-coding sequences (Release)</option>
137 <option value="sample">Samples</option>
138 <option value="environmental">Environmental samples</option>
139 <option value="read_run">Raw reads</option>
140 <option value="read_study">Raw reads (grouped by study)</option>
141 <option value="read_experiment">Raw reads (grouped by experiment)</option>
142 <option value="analysis">Nucleotide sequence analyses from reads</option>
143 <option value="sequence_update">Nucleotide sequences (Update)</option>
144 <option value="coding_update">Protein-coding sequences (Update)</option>
145 <option value="tsa_set">Transcriptome assembly contig set</option>
146 <option value="analysis_study">Nucleotide sequence analyses from reads (grouped by study)</option>
147 <option value="noncoding_update">Non-coding sequences (Update)</option>
148 </param>
149 <when value="noncoding_release">
150 <conditional name="display_opt">
151 <param argument="--display" type="select" label="Display option to specify the display format">
152 <expand macro="display_options"/>
153 </param>
154 <when value="xml">
155 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
156 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
157 </when>
158 <when value="text">
159 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
160 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
161 </when>
162 <when value="fastq"/>
163 <when value="html">
164 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
165 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
166 </when>
167 <when value="report">
168 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
169 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
170 <param argument="--fields" type="select" multiple="true" label="Fields to return">
171 <option value="accession">accession</option>
172 <option value="base_count">base_count</option>
173 <option value="collected_by">collected_by</option>
174 <option value="dataclass">dataclass</option>
175 <option value="first_public">first_public</option>
176 <option value="last_updated">last_updated</option>
177 <option value="location">location</option>
178 <option value="tax_division">tax_division</option>
179 <option value="tax_id">tax_id</option>
180 <option value="scientific_name">scientific_name</option>
181 <option value="rna_class">rna_class</option>
182 <option value="gene">gene</option>
183 <option value="gene_synonym">gene_synonym</option>
184 <option value="product">product</option>
185 <option value="anticodon">anticodon</option>
186 <option value="function">function</option>
187 <option value="locus_tag">locus_tag</option>
188 <option value="experiment">experiment</option>
189 <option value="inference">inference</option>
190 <option value="note">note</option>
191 <option value="bio_material">bio_material</option>
192 <option value="cell_line">cell_line</option>
193 <option value="cell_type">cell_type</option>
194 <option value="country">country</option>
195 <option value="cultivar">cultivar</option>
196 <option value="culture_collection">culture_collection</option>
197 <option value="description">description</option>
198 <option value="dev_stage">dev_stage</option>
199 <option value="ecotype">ecotype</option>
200 <option value="environmental_sample">environmental_sample</option>
201 <option value="germline">germline</option>
202 <option value="host">host</option>
203 <option value="identified_by">identified_by</option>
204 <option value="isolate">isolate</option>
205 <option value="isolation_source">isolation_source</option>
206 <option value="keywords">keywords</option>
207 <option value="lab_host">lab_host</option>
208 <option value="mating_type">mating_type</option>
209 <option value="mol_type">mol_type</option>
210 <option value="organelle">organelle</option>
211 <option value="serotype">serotype</option>
212 <option value="serovar">serovar</option>
213 <option value="sex">sex</option>
214 <option value="collection_date">collection_date</option>
215 <option value="submitted_sex">submitted_sex</option>
216 <option value="specimen_voucher">specimen_voucher</option>
217 <option value="strain">strain</option>
218 <option value="sub_species">sub_species</option>
219 <option value="sub_strain">sub_strain</option>
220 <option value="tissue_lib">tissue_lib</option>
221 <option value="tissue_type">tissue_type</option>
222 <option value="topology">topology</option>
223 <option value="variety">variety</option>
224 <option value="sequence_md5">sequence_md5</option>
225 <option value="study_accession">study_accession</option>
226 </param>
227 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
228 <option value="mol_type">in vivo molecule type of the sequence</option>
229 <option value="last_updated">date when last updated</option>
230 <option value="sequence_md5"></option>
231 <option value="collected_by">name of the person who collected the specimen</option>
232 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
233 <option value="sex">sex of the organism from which the sample was obtained</option>
234 <option value="keywords">keywords associated with sequence</option>
235 <option value="cell_line">cell line from which the sample was obtained</option>
236 <option value="inference">a structured description of non-experimental evidence</option>
237 <option value="bio_material">identifier for biological material including institute and collection code</option>
238 <option value="identified_by">name of the taxonomist who identified the specimen</option>
239 <option value="note">any comment or additional information</option>
240 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
241 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
242 <option value="tax_division">taxonomic division</option>
243 <option value="collection_date">date that the specimen was collected</option>
244 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
245 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
246 <option value="isolate">individual isolate from which sample was obtained</option>
247 <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option>
248 <option value="experiment">a brief description of the nature of the experimental evidence</option>
249 <option value="location">geographic location of isolation of the sample</option>
250 <option value="study_accession">study accession number</option>
251 <option value="function">function attributed to a sequence</option>
252 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
253 <option value="product">name of the product associated with the feature</option>
254 <option value="description">brief sequence description</option>
255 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
256 <option value="cell_type">cell type from which the sample was obtained</option>
257 <option value="accession">accession number</option>
258 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
259 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
260 <option value="tissue_type">tissue type from which the sample was obtained</option>
261 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
262 <option value="tissue_lib">tissue library from which sample was obtained</option>
263 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
264 <option value="base_count">number of base pairs</option>
265 <option value="topology">sequence topology: circular or linear</option>
266 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
267 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
268 <option value="first_public">date when made public</option>
269 <option value="strain">strain from which sample was obtained</option>
270 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
271 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
272 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
273 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
274 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
275 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
276 <option value="rna_class">classification of RNA</option>
277 <option value="dataclass">sequence data class</option>
278 <option value="gene">symbol of the gene corresponding to a sequence region</option>
279 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
280 </param>
281 </when>
282 <when value="fasta"/>
283 </conditional>
284 </when>
285 <when value="assembly">
286 <conditional name="display_opt">
287 <param argument="--display" type="select" label="Display option to specify the display format">
288 <expand macro="display_options"/>
289 </param>
290 <when value="xml">
291 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
292 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
293 </when>
294 <when value="text">
295 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
296 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
297 </when>
298 <when value="fastq"/>
299 <when value="html">
300 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
301 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
302 </when>
303 <when value="report">
304 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
305 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
306 <param argument="--fields" type="select" multiple="true" label="Fields to return">
307 <option value="accession">accession</option>
308 <option value="study_accession">study_accession</option>
309 <option value="sample_accession">sample_accession</option>
310 <option value="assembly_name">assembly_name</option>
311 <option value="assembly_title">assembly_title</option>
312 <option value="study_name">study_name</option>
313 <option value="study_title">study_title</option>
314 <option value="study_description">study_description</option>
315 <option value="tax_id">tax_id</option>
316 <option value="scientific_name">scientific_name</option>
317 <option value="strain">strain</option>
318 <option value="base_count">base_count</option>
319 <option value="assembly_level">assembly_level</option>
320 <option value="genome_representation">genome_representation</option>
321 </param>
322 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
323 <option value="assembly_name">genome assembly name for all live versions</option>
324 <option value="base_count">number of base pairs</option>
325 <option value="strain">strain from which sample was obtained</option>
326 <option value="study_description">detailed sequencing study description</option>
327 <option value="accession">accession number</option>
328 <option value="assembly_level">assembly level</option>
329 <option value="sample_accession">sample accession number</option>
330 <option value="assembly_title">brief genome assembly description</option>
331 <option value="study_title">brief sequencing study description</option>
332 <option value="genome_representation">whether this is a full or partial genome</option>
333 <option value="study_name">sequencing study name</option>
334 <option value="study_accession">study accession number</option>
335 </param>
336 </when>
337 <when value="fasta"/>
338 </conditional>
339 </when>
340 <when value="sequence_release">
341 <conditional name="display_opt">
342 <param argument="--display" type="select" label="Display option to specify the display format">
343 <expand macro="display_options"/>
344 </param>
345 <when value="xml">
346 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
347 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
348 </when>
349 <when value="text">
350 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
351 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
352 </when>
353 <when value="fastq"/>
354 <when value="html">
355 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
356 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
357 </when>
358 <when value="report">
359 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
360 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
361 <param argument="--fields" type="select" multiple="true" label="Fields to return">
362 <option value="accession">accession</option>
363 <option value="base_count">base_count</option>
364 <option value="bio_material">bio_material</option>
365 <option value="cell_line">cell_line</option>
366 <option value="cell_type">cell_type</option>
367 <option value="collected_by">collected_by</option>
368 <option value="collection_date">collection_date</option>
369 <option value="country">country</option>
370 <option value="cultivar">cultivar</option>
371 <option value="culture_collection">culture_collection</option>
372 <option value="dataclass">dataclass</option>
373 <option value="description">description</option>
374 <option value="dev_stage">dev_stage</option>
375 <option value="ecotype">ecotype</option>
376 <option value="environmental_sample">environmental_sample</option>
377 <option value="first_public">first_public</option>
378 <option value="germline">germline</option>
379 <option value="host">host</option>
380 <option value="identified_by">identified_by</option>
381 <option value="isolate">isolate</option>
382 <option value="isolation_source">isolation_source</option>
383 <option value="keywords">keywords</option>
384 <option value="lab_host">lab_host</option>
385 <option value="last_updated">last_updated</option>
386 <option value="location">location</option>
387 <option value="mating_type">mating_type</option>
388 <option value="mol_type">mol_type</option>
389 <option value="organelle">organelle</option>
390 <option value="serotype">serotype</option>
391 <option value="serovar">serovar</option>
392 <option value="sex">sex</option>
393 <option value="submitted_sex">submitted_sex</option>
394 <option value="specimen_voucher">specimen_voucher</option>
395 <option value="strain">strain</option>
396 <option value="sub_species">sub_species</option>
397 <option value="sub_strain">sub_strain</option>
398 <option value="tax_division">tax_division</option>
399 <option value="tissue_lib">tissue_lib</option>
400 <option value="tissue_type">tissue_type</option>
401 <option value="topology">topology</option>
402 <option value="variety">variety</option>
403 <option value="tax_id">tax_id</option>
404 <option value="scientific_name">scientific_name</option>
405 <option value="altitude">altitude</option>
406 <option value="haplotype">haplotype</option>
407 <option value="plasmid">plasmid</option>
408 <option value="study_accession">study_accession</option>
409 <option value="sequence_md5">sequence_md5</option>
410 </param>
411 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
412 <option value="mol_type">in vivo molecule type of the sequence</option>
413 <option value="last_updated">date when last updated</option>
414 <option value="sequence_md5"></option>
415 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
416 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
417 <option value="sex">sex of the organism from which the sample was obtained</option>
418 <option value="keywords">keywords associated with sequence</option>
419 <option value="collected_by">name of the person who collected the specimen</option>
420 <option value="cell_line">cell line from which the sample was obtained</option>
421 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
422 <option value="bio_material">identifier for biological material including institute and collection code</option>
423 <option value="identified_by">name of the taxonomist who identified the specimen</option>
424 <option value="cell_type">cell type from which the sample was obtained</option>
425 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
426 <option value="tax_division">taxonomic division</option>
427 <option value="collection_date">date that the specimen was collected</option>
428 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
429 <option value="altitude">Altitude (m)</option>
430 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
431 <option value="isolate">individual isolate from which sample was obtained</option>
432 <option value="location">geographic location of isolation of the sample</option>
433 <option value="study_accession">study accession number</option>
434 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
435 <option value="description">brief sequence description</option>
436 <option value="accession">accession number</option>
437 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
438 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
439 <option value="tissue_type">tissue type from which the sample was obtained</option>
440 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
441 <option value="tissue_lib">tissue library from which sample was obtained</option>
442 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
443 <option value="base_count">number of base pairs</option>
444 <option value="topology">sequence topology: circular or linear</option>
445 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
446 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
447 <option value="first_public">date when made public</option>
448 <option value="strain">strain from which sample was obtained</option>
449 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
450 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
451 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
452 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
453 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
454 <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option>
455 <option value="dataclass">sequence data class</option>
456 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
457 </param>
458 </when>
459 <when value="fasta"/>
460 </conditional>
461 </when>
462 <when value="wgs_set">
463 <conditional name="display_opt">
464 <param argument="--display" type="select" label="Display option to specify the display format">
465 <expand macro="display_options"/>
466 </param>
467 <when value="xml">
468 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
469 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
470 </when>
471 <when value="text">
472 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
473 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
474 </when>
475 <when value="fastq"/>
476 <when value="html">
477 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
478 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
479 </when>
480 <when value="report">
481 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
482 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
483 <param argument="--fields" type="select" multiple="true" label="Fields to return">
484 <option value="accession">accession</option>
485 <option value="bio_material">bio_material</option>
486 <option value="cell_line">cell_line</option>
487 <option value="cell_type">cell_type</option>
488 <option value="collected_by">collected_by</option>
489 <option value="collection_date">collection_date</option>
490 <option value="country">country</option>
491 <option value="cultivar">cultivar</option>
492 <option value="culture_collection">culture_collection</option>
493 <option value="description">description</option>
494 <option value="dev_stage">dev_stage</option>
495 <option value="ecotype">ecotype</option>
496 <option value="environmental_sample">environmental_sample</option>
497 <option value="first_public">first_public</option>
498 <option value="germline">germline</option>
499 <option value="host">host</option>
500 <option value="identified_by">identified_by</option>
501 <option value="isolate">isolate</option>
502 <option value="isolation_source">isolation_source</option>
503 <option value="keywords">keywords</option>
504 <option value="lab_host">lab_host</option>
505 <option value="last_updated">last_updated</option>
506 <option value="location">location</option>
507 <option value="mating_type">mating_type</option>
508 <option value="mol_type">mol_type</option>
509 <option value="serotype">serotype</option>
510 <option value="serovar">serovar</option>
511 <option value="sex">sex</option>
512 <option value="submitted_sex">submitted_sex</option>
513 <option value="specimen_voucher">specimen_voucher</option>
514 <option value="strain">strain</option>
515 <option value="sub_species">sub_species</option>
516 <option value="sub_strain">sub_strain</option>
517 <option value="tax_division">tax_division</option>
518 <option value="tissue_lib">tissue_lib</option>
519 <option value="tissue_type">tissue_type</option>
520 <option value="variety">variety</option>
521 <option value="tax_id">tax_id</option>
522 <option value="scientific_name">scientific_name</option>
523 <option value="altitude">altitude</option>
524 <option value="haplotype">haplotype</option>
525 <option value="study_accession">study_accession</option>
526 <option value="set_files">set_files</option>
527 </param>
528 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
529 <option value="mol_type">in vivo molecule type of the sequence</option>
530 <option value="last_updated">date when last updated</option>
531 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
532 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
533 <option value="accession">accession number</option>
534 <option value="sex">sex of the organism from which the sample was obtained</option>
535 <option value="cell_line">cell line from which the sample was obtained</option>
536 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
537 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
538 <option value="bio_material">identifier for biological material including institute and collection code</option>
539 <option value="identified_by">name of the taxonomist who identified the specimen</option>
540 <option value="cell_type">cell type from which the sample was obtained</option>
541 <option value="tax_division">taxonomic division</option>
542 <option value="collection_date">date that the specimen was collected</option>
543 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
544 <option value="altitude">Altitude (m)</option>
545 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
546 <option value="isolate">individual isolate from which sample was obtained</option>
547 <option value="location">geographic location of isolation of the sample</option>
548 <option value="study_accession">study accession number</option>
549 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
550 <option value="description">brief sequence description</option>
551 <option value="tissue_lib">tissue library from which sample was obtained</option>
552 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
553 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
554 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
555 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
556 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
557 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
558 <option value="collected_by">name of the person who collected the specimen</option>
559 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
560 <option value="first_public">date when made public</option>
561 <option value="strain">strain from which sample was obtained</option>
562 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
563 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
564 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
565 <option value="tissue_type">tissue type from which the sample was obtained</option>
566 <option value="keywords">keywords associated with sequence</option>
567 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
568 </param>
569 </when>
570 <when value="fasta"/>
571 </conditional>
572 </when>
573 <when value="study">
574 <conditional name="display_opt">
575 <param argument="--display" type="select" label="Display option to specify the display format">
576 <expand macro="display_options"/>
577 </param>
578 <when value="xml">
579 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
580 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
581 </when>
582 <when value="text">
583 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
584 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
585 </when>
586 <when value="fastq"/>
587 <when value="html">
588 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
589 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
590 </when>
591 <when value="report">
592 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
593 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
594 <param argument="--fields" type="select" multiple="true" label="Fields to return">
595 <option value="study_accession">study_accession</option>
596 <option value="secondary_study_accession">secondary_study_accession</option>
597 <option value="study_description">study_description</option>
598 <option value="study_name">study_name</option>
599 <option value="study_title">study_title</option>
600 <option value="tax_id">tax_id</option>
601 <option value="scientific_name">scientific_name</option>
602 <option value="strain">strain</option>
603 <option value="breed">breed</option>
604 <option value="cultivar">cultivar</option>
605 <option value="isolate">isolate</option>
606 <option value="center_name">center_name</option>
607 <option value="broker_name">broker_name</option>
608 <option value="keywords">keywords</option>
609 <option value="geo_accession">geo_accession</option>
610 <option value="last_updated">last_updated</option>
611 </param>
612 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
613 <option value="broker_name">broker name</option>
614 <option value="last_updated">date when last updated</option>
615 <option value="center_name">Submitting center</option>
616 <option value="study_description">detailed sequencing study description</option>
617 <option value="breed">breed</option>
618 <option value="isolate">individual isolate from which sample was obtained</option>
619 <option value="study_name">sequencing study name</option>
620 <option value="geo_accession">GEO accession</option>
621 <option value="strain">strain from which sample was obtained</option>
622 <option value="secondary_study_accession">project accession number</option>
623 <option value="keywords">keywords associated with sequence</option>
624 <option value="study_title">brief sequencing study description</option>
625 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
626 <option value="study_accession">study accession number</option>
627 </param>
628 </when>
629 <when value="fasta"/>
630 </conditional>
631 </when>
632 <when value="taxon">
633 <conditional name="display_opt">
634 <param argument="--display" type="select" label="Display option to specify the display format">
635 <expand macro="display_options"/>
636 </param>
637 <when value="xml">
638 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
639 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
640 </when>
641 <when value="text">
642 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
643 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
644 </when>
645 <when value="fastq"/>
646 <when value="html">
647 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
648 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
649 </when>
650 <when value="report">
651 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
652 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
653 <param argument="--fields" type="select" multiple="true" label="Fields to return">
654 <option value="tax_id">tax_id</option>
655 <option value="taxon_title">taxon_title</option>
656 <option value="scientific_name">scientific_name</option>
657 </param>
658 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
659 </param>
660 </when>
661 <when value="fasta"/>
662 </conditional>
663 </when>
664 <when value="coding_release">
665 <conditional name="display_opt">
666 <param argument="--display" type="select" label="Display option to specify the display format">
667 <expand macro="display_options"/>
668 </param>
669 <when value="xml">
670 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
671 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
672 </when>
673 <when value="text">
674 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
675 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
676 </when>
677 <when value="fastq"/>
678 <when value="html">
679 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
680 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
681 </when>
682 <when value="report">
683 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
684 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
685 <param argument="--fields" type="select" multiple="true" label="Fields to return">
686 <option value="accession">accession</option>
687 <option value="base_count">base_count</option>
688 <option value="bio_material">bio_material</option>
689 <option value="cell_line">cell_line</option>
690 <option value="cell_type">cell_type</option>
691 <option value="collected_by">collected_by</option>
692 <option value="collection_date">collection_date</option>
693 <option value="country">country</option>
694 <option value="cultivar">cultivar</option>
695 <option value="culture_collection">culture_collection</option>
696 <option value="dataclass">dataclass</option>
697 <option value="description">description</option>
698 <option value="dev_stage">dev_stage</option>
699 <option value="ecotype">ecotype</option>
700 <option value="environmental_sample">environmental_sample</option>
701 <option value="first_public">first_public</option>
702 <option value="germline">germline</option>
703 <option value="host">host</option>
704 <option value="identified_by">identified_by</option>
705 <option value="isolate">isolate</option>
706 <option value="isolation_source">isolation_source</option>
707 <option value="keywords">keywords</option>
708 <option value="lab_host">lab_host</option>
709 <option value="last_updated">last_updated</option>
710 <option value="location">location</option>
711 <option value="mating_type">mating_type</option>
712 <option value="mol_type">mol_type</option>
713 <option value="organelle">organelle</option>
714 <option value="serotype">serotype</option>
715 <option value="serovar">serovar</option>
716 <option value="sex">sex</option>
717 <option value="submitted_sex">submitted_sex</option>
718 <option value="specimen_voucher">specimen_voucher</option>
719 <option value="strain">strain</option>
720 <option value="sub_species">sub_species</option>
721 <option value="sub_strain">sub_strain</option>
722 <option value="tax_division">tax_division</option>
723 <option value="tissue_lib">tissue_lib</option>
724 <option value="tissue_type">tissue_type</option>
725 <option value="variety">variety</option>
726 <option value="allele">allele</option>
727 <option value="artificial_location">artificial_location</option>
728 <option value="codon_start">codon_start</option>
729 <option value="ec_number">ec_number</option>
730 <option value="exception">exception</option>
731 <option value="experiment">experiment</option>
732 <option value="function">function</option>
733 <option value="topology">topology</option>
734 <option value="gene">gene</option>
735 <option value="gene_synonym">gene_synonym</option>
736 <option value="inference">inference</option>
737 <option value="locus_tag">locus_tag</option>
738 <option value="map">map</option>
739 <option value="note">note</option>
740 <option value="old_locus_tag">old_locus_tag</option>
741 <option value="operon">operon</option>
742 <option value="partial">partial</option>
743 <option value="product">product</option>
744 <option value="protein_id">protein_id</option>
745 <option value="pseudo">pseudo</option>
746 <option value="pseudo_gene">pseudo_gene</option>
747 <option value="ribosomal_slippage">ribosomal_slippage</option>
748 <option value="standard_name">standard_name</option>
749 <option value="trans_splicing">trans_splicing</option>
750 <option value="transl_except">transl_except</option>
751 <option value="transl_table">transl_table</option>
752 <option value="tax_id">tax_id</option>
753 <option value="scientific_name">scientific_name</option>
754 <option value="parent_accession">parent_accession</option>
755 <option value="altitude">altitude</option>
756 <option value="haplotype">haplotype</option>
757 <option value="sequence_md5">sequence_md5</option>
758 </param>
759 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
760 <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option>
761 <option value="mol_type">in vivo molecule type of the sequence</option>
762 <option value="last_updated">date when last updated</option>
763 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
764 <option value="transl_except">a single codon translation that does not conform to genetic code</option>
765 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
766 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
767 <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option>
768 <option value="sex">sex of the organism from which the sample was obtained</option>
769 <option value="pseudo_gene">indicates that this feature is a pseudogene</option>
770 <option value="standard_name">accepted standard name for a feature</option>
771 <option value="collected_by">name of the person who collected the specimen</option>
772 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
773 <option value="cell_type">cell type from which the sample was obtained</option>
774 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
775 <option value="inference">a structured description of non-experimental evidence</option>
776 <option value="bio_material">identifier for biological material including institute and collection code</option>
777 <option value="parent_accession">parent sequence accession number</option>
778 <option value="identified_by">name of the taxonomist who identified the specimen</option>
779 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
780 <option value="sequence_md5"></option>
781 <option value="tax_division">taxonomic division</option>
782 <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
783 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
784 <option value="altitude">Altitude (m)</option>
785 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
786 <option value="isolate">individual isolate from which sample was obtained</option>
787 <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option>
788 <option value="note">any comment or additional information</option>
789 <option value="experiment">a brief description of the nature of the experimental evidence</option>
790 <option value="location">geographic location of isolation of the sample</option>
791 <option value="collection_date">date that the specimen was collected</option>
792 <option value="allele">name of the allele for the given gene</option>
793 <option value="protein_id">a stable protein identifier issued by INSDC</option>
794 <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option>
795 <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option>
796 <option value="function">function attributed to a sequence</option>
797 <option value="map">genomic map position of feature</option>
798 <option value="product">name of the product associated with the feature</option>
799 <option value="description">brief sequence description</option>
800 <option value="cell_line">cell line from which the sample was obtained</option>
801 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
802 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
803 <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option>
804 <option value="accession">accession number</option>
805 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
806 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
807 <option value="tissue_type">tissue type from which the sample was obtained</option>
808 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
809 <option value="tissue_lib">tissue library from which sample was obtained</option>
810 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
811 <option value="base_count">number of base pairs</option>
812 <option value="topology">sequence topology: circular or linear</option>
813 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
814 <option value="first_public">date when made public</option>
815 <option value="strain">strain from which sample was obtained</option>
816 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
817 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
818 <option value="pseudo">the feature is non-functional</option>
819 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
820 <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option>
821 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
822 <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option>
823 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
824 <option value="keywords">keywords associated with sequence</option>
825 <option value="dataclass">sequence data class</option>
826 <option value="gene">symbol of the gene corresponding to a sequence region</option>
827 <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option>
828 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
829 </param>
830 </when>
831 <when value="fasta"/>
832 </conditional>
833 </when>
834 <when value="sample">
835 <conditional name="display_opt">
836 <param argument="--display" type="select" label="Display option to specify the display format">
837 <expand macro="display_options"/>
838 </param>
839 <when value="xml">
840 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
841 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
842 </when>
843 <when value="text">
844 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
845 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
846 </when>
847 <when value="fastq"/>
848 <when value="html">
849 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
850 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
851 </when>
852 <when value="report">
853 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
854 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
855 <param argument="--fields" type="select" multiple="true" label="Fields to return">
856 <option value="accession">accession</option>
857 <option value="secondary_sample_accession">secondary_sample_accession</option>
858 <option value="bio_material">bio_material</option>
859 <option value="cell_line">cell_line</option>
860 <option value="cell_type">cell_type</option>
861 <option value="collected_by">collected_by</option>
862 <option value="collection_date">collection_date</option>
863 <option value="country">country</option>
864 <option value="cultivar">cultivar</option>
865 <option value="culture_collection">culture_collection</option>
866 <option value="description">description</option>
867 <option value="dev_stage">dev_stage</option>
868 <option value="ecotype">ecotype</option>
869 <option value="environmental_sample">environmental_sample</option>
870 <option value="first_public">first_public</option>
871 <option value="germline">germline</option>
872 <option value="identified_by">identified_by</option>
873 <option value="isolate">isolate</option>
874 <option value="isolation_source">isolation_source</option>
875 <option value="location">location</option>
876 <option value="mating_type">mating_type</option>
877 <option value="serotype">serotype</option>
878 <option value="serovar">serovar</option>
879 <option value="sex">sex</option>
880 <option value="submitted_sex">submitted_sex</option>
881 <option value="specimen_voucher">specimen_voucher</option>
882 <option value="strain">strain</option>
883 <option value="sub_species">sub_species</option>
884 <option value="sub_strain">sub_strain</option>
885 <option value="tissue_lib">tissue_lib</option>
886 <option value="tissue_type">tissue_type</option>
887 <option value="variety">variety</option>
888 <option value="tax_id">tax_id</option>
889 <option value="scientific_name">scientific_name</option>
890 <option value="sample_alias">sample_alias</option>
891 <option value="checklist">checklist</option>
892 <option value="center_name">center_name</option>
893 <option value="depth">depth</option>
894 <option value="elevation">elevation</option>
895 <option value="altitude">altitude</option>
896 <option value="environment_biome">environment_biome</option>
897 <option value="environment_feature">environment_feature</option>
898 <option value="environment_material">environment_material</option>
899 <option value="temperature">temperature</option>
900 <option value="salinity">salinity</option>
901 <option value="sampling_campaign">sampling_campaign</option>
902 <option value="sampling_site">sampling_site</option>
903 <option value="sampling_platform">sampling_platform</option>
904 <option value="protocol_label">protocol_label</option>
905 <option value="project_name">project_name</option>
906 <option value="host">host</option>
907 <option value="host_tax_id">host_tax_id</option>
908 <option value="host_status">host_status</option>
909 <option value="host_sex">host_sex</option>
910 <option value="submitted_host_sex">submitted_host_sex</option>
911 <option value="host_body_site">host_body_site</option>
912 <option value="host_gravidity">host_gravidity</option>
913 <option value="host_phenotype">host_phenotype</option>
914 <option value="host_genotype">host_genotype</option>
915 <option value="host_growth_conditions">host_growth_conditions</option>
916 <option value="environmental_package">environmental_package</option>
917 <option value="investigation_type">investigation_type</option>
918 <option value="experimental_factor">experimental_factor</option>
919 <option value="sample_collection">sample_collection</option>
920 <option value="sequencing_method">sequencing_method</option>
921 <option value="target_gene">target_gene</option>
922 <option value="ph">ph</option>
923 <option value="broker_name">broker_name</option>
924 </param>
925 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
926 <option value="secondary_sample_accession">secondary sample accession number</option>
927 <option value="environment_material">Environment (Material)</option>
928 <option value="host_sex">physical sex of the host</option>
929 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
930 <option value="center_name">Submitting center</option>
931 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
932 <option value="sex">sex of the organism from which the sample was obtained</option>
933 <option value="host_phenotype">phenotype of host</option>
934 <option value="sampling_site">the site/station where this sample was collection</option>
935 <option value="sequencing_method">sequencing method used</option>
936 <option value="cell_line">cell line from which the sample was obtained</option>
937 <option value="bio_material">identifier for biological material including institute and collection code</option>
938 <option value="target_gene">targeted gene or locus name for marker gene studies</option>
939 <option value="experimental_factor">variable aspects of the experimental design</option>
940 <option value="identified_by">name of the taxonomist who identified the specimen</option>
941 <option value="cell_type">cell type from which the sample was obtained</option>
942 <option value="temperature">Temperature (C)</option>
943 <option value="sampling_platform">the large infrastructure from which this sample was collected</option>
944 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
945 <option value="collection_date">date that the specimen was collected</option>
946 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
947 <option value="altitude">Altitude (m)</option>
948 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
949 <option value="isolate">individual isolate from which sample was obtained</option>
950 <option value="investigation_type">the study type targeted by the sequencing</option>
951 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
952 <option value="protocol_label">the protocol used to produce the sample</option>
953 <option value="location">geographic location of isolation of the sample</option>
954 <option value="host_genotype">genotype of host</option>
955 <option value="ph">pH</option>
956 <option value="broker_name">broker name</option>
957 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
958 <option value="project_name">name of the project within which the sequencing was organized</option>
959 <option value="elevation">Elevation (m)</option>
960 <option value="description">brief sequence description</option>
961 <option value="sample_alias">submitter's name for the sample</option>
962 <option value="checklist">checklist name (or ID)</option>
963 <option value="sampling_campaign">the activity within which this sample was collected</option>
964 <option value="accession">accession number</option>
965 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
966 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
967 <option value="tissue_type">tissue type from which the sample was obtained</option>
968 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
969 <option value="tissue_lib">tissue library from which sample was obtained</option>
970 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
971 <option value="environment_biome">Environment (Biome)</option>
972 <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option>
973 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
974 <option value="first_public">date when made public</option>
975 <option value="environment_feature">Environment (Feature)</option>
976 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
977 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
978 <option value="collected_by">name of the person who collected the specimen</option>
979 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
980 <option value="salinity">Salinity (PSU)</option>
981 <option value="host_status">condition of host (eg. diseased or healthy)</option>
982 <option value="strain">strain from which sample was obtained</option>
983 <option value="depth">Depth (m)</option>
984 <option value="host_tax_id">NCBI taxon id of the host</option>
985 <option value="host_body_site">name of body site from where the sample was obtained</option>
986 <option value="host_growth_conditions">literature reference giving growth conditions of the host</option>
987 <option value="sample_collection">the method or deviced employed for collecting the sample</option>
988 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
989 </param>
990 </when>
991 <when value="fasta"/>
992 </conditional>
993 </when>
994 <when value="environmental">
995 <conditional name="display_opt">
996 <param argument="--display" type="select" label="Display option to specify the display format">
997 <expand macro="display_options"/>
998 </param>
999 <when value="xml">
1000 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1001 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1002 </when>
1003 <when value="text">
1004 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1005 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1006 </when>
1007 <when value="fastq"/>
1008 <when value="html">
1009 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1010 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1011 </when>
1012 <when value="report">
1013 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1014 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1015 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1016 <option value="accession">accession</option>
1017 <option value="secondary_sample_accession">secondary_sample_accession</option>
1018 <option value="bio_material">bio_material</option>
1019 <option value="cell_line">cell_line</option>
1020 <option value="collected_by">collected_by</option>
1021 <option value="collection_date">collection_date</option>
1022 <option value="country">country</option>
1023 <option value="marine_region">marine_region</option>
1024 <option value="cultivar">cultivar</option>
1025 <option value="description">description</option>
1026 <option value="dev_stage">dev_stage</option>
1027 <option value="first_public">first_public</option>
1028 <option value="identified_by">identified_by</option>
1029 <option value="isolation_source">isolation_source</option>
1030 <option value="location">location</option>
1031 <option value="strain">strain</option>
1032 <option value="tissue_type">tissue_type</option>
1033 <option value="tax_id">tax_id</option>
1034 <option value="scientific_name">scientific_name</option>
1035 <option value="sample_alias">sample_alias</option>
1036 <option value="checklist">checklist</option>
1037 <option value="center_name">center_name</option>
1038 <option value="depth">depth</option>
1039 <option value="elevation">elevation</option>
1040 <option value="altitude">altitude</option>
1041 <option value="environment_biome">environment_biome</option>
1042 <option value="environment_feature">environment_feature</option>
1043 <option value="environment_material">environment_material</option>
1044 <option value="temperature">temperature</option>
1045 <option value="salinity">salinity</option>
1046 <option value="sampling_campaign">sampling_campaign</option>
1047 <option value="sampling_site">sampling_site</option>
1048 <option value="sampling_platform">sampling_platform</option>
1049 <option value="protocol_label">protocol_label</option>
1050 <option value="project_name">project_name</option>
1051 <option value="host">host</option>
1052 <option value="host_tax_id">host_tax_id</option>
1053 <option value="host_status">host_status</option>
1054 <option value="host_sex">host_sex</option>
1055 <option value="submitted_host_sex">submitted_host_sex</option>
1056 <option value="host_body_site">host_body_site</option>
1057 <option value="host_gravidity">host_gravidity</option>
1058 <option value="host_phenotype">host_phenotype</option>
1059 <option value="host_genotype">host_genotype</option>
1060 <option value="host_growth_conditions">host_growth_conditions</option>
1061 <option value="environmental_package">environmental_package</option>
1062 <option value="investigation_type">investigation_type</option>
1063 <option value="experimental_factor">experimental_factor</option>
1064 <option value="sample_collection">sample_collection</option>
1065 <option value="sequencing_method">sequencing_method</option>
1066 <option value="target_gene">target_gene</option>
1067 <option value="ph">ph</option>
1068 <option value="broker_name">broker_name</option>
1069 <option value="event_label">event_label</option>
1070 </param>
1071 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1072 <option value="secondary_sample_accession">secondary sample accession number</option>
1073 <option value="environment_material">Environment (Material)</option>
1074 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
1075 <option value="event_label">label given to sampling event</option>
1076 <option value="center_name">Submitting center</option>
1077 <option value="accession">accession number</option>
1078 <option value="host_phenotype">phenotype of host</option>
1079 <option value="cell_line">cell line from which the sample was obtained</option>
1080 <option value="bio_material">identifier for biological material including institute and collection code</option>
1081 <option value="target_gene">targeted gene or locus name for marker gene studies</option>
1082 <option value="experimental_factor">variable aspects of the experimental design</option>
1083 <option value="identified_by">name of the taxonomist who identified the specimen</option>
1084 <option value="temperature">Temperature (C)</option>
1085 <option value="sampling_platform">the large infrastructure from which this sample was collected</option>
1086 <option value="collected_by">name of the person who collected the specimen</option>
1087 <option value="collection_date">date that the specimen was collected</option>
1088 <option value="altitude">Altitude (m)</option>
1089 <option value="host_sex">physical sex of the host</option>
1090 <option value="investigation_type">the study type targeted by the sequencing</option>
1091 <option value="location">geographic location of isolation of the sample</option>
1092 <option value="host_genotype">genotype of host</option>
1093 <option value="ph">pH</option>
1094 <option value="broker_name">broker name</option>
1095 <option value="project_name">name of the project within which the sequencing was organized</option>
1096 <option value="elevation">Elevation (m)</option>
1097 <option value="description">brief sequence description</option>
1098 <option value="sample_alias">submitter's name for the sample</option>
1099 <option value="checklist">checklist name (or ID)</option>
1100 <option value="sampling_campaign">the activity within which this sample was collected</option>
1101 <option value="protocol_label">the protocol used to produce the sample</option>
1102 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
1103 <option value="sampling_site">the site/station where this sample was collection</option>
1104 <option value="host_tax_id">NCBI taxon id of the host</option>
1105 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
1106 <option value="environment_biome">Environment (Biome)</option>
1107 <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option>
1108 <option value="marine_region">geographical origin of the sample as defined by the marine region</option>
1109 <option value="first_public">date when made public</option>
1110 <option value="environment_feature">Environment (Feature)</option>
1111 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
1112 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
1113 <option value="salinity">Salinity (PSU)</option>
1114 <option value="host_status">condition of host (eg. diseased or healthy)</option>
1115 <option value="strain">strain from which sample was obtained</option>
1116 <option value="depth">Depth (m)</option>
1117 <option value="tissue_type">tissue type from which the sample was obtained</option>
1118 <option value="host_body_site">name of body site from where the sample was obtained</option>
1119 <option value="host_growth_conditions">literature reference giving growth conditions of the host</option>
1120 <option value="sample_collection">the method or deviced employed for collecting the sample</option>
1121 <option value="sequencing_method">sequencing method used</option>
1122 </param>
1123 </when>
1124 <when value="fasta"/>
1125 </conditional>
1126 </when>
1127 <when value="read_run">
1128 <conditional name="display_opt">
1129 <param argument="--display" type="select" label="Display option to specify the display format">
1130 <expand macro="display_options"/>
1131 </param>
1132 <when value="xml">
1133 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1134 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1135 </when>
1136 <when value="text">
1137 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1138 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1139 </when>
1140 <when value="fastq"/>
1141 <when value="html">
1142 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1143 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1144 </when>
1145 <when value="report">
1146 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1147 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1148 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1149 <option value="study_accession">study_accession</option>
1150 <option value="secondary_study_accession">secondary_study_accession</option>
1151 <option value="sample_accession">sample_accession</option>
1152 <option value="secondary_sample_accession">secondary_sample_accession</option>
1153 <option value="experiment_accession">experiment_accession</option>
1154 <option value="run_accession">run_accession</option>
1155 <option value="submission_accession">submission_accession</option>
1156 <option value="tax_id">tax_id</option>
1157 <option value="scientific_name">scientific_name</option>
1158 <option value="instrument_platform">instrument_platform</option>
1159 <option value="instrument_model">instrument_model</option>
1160 <option value="library_name">library_name</option>
1161 <option value="nominal_length">nominal_length</option>
1162 <option value="library_layout">library_layout</option>
1163 <option value="library_strategy">library_strategy</option>
1164 <option value="library_source">library_source</option>
1165 <option value="library_selection">library_selection</option>
1166 <option value="read_count">read_count</option>
1167 <option value="base_count">base_count</option>
1168 <option value="center_name">center_name</option>
1169 <option value="first_public">first_public</option>
1170 <option value="last_updated">last_updated</option>
1171 <option value="experiment_title">experiment_title</option>
1172 <option value="study_title">study_title</option>
1173 <option value="study_alias">study_alias</option>
1174 <option value="experiment_alias">experiment_alias</option>
1175 <option value="run_alias">run_alias</option>
1176 <option value="fastq_bytes">fastq_bytes</option>
1177 <option value="fastq_md5">fastq_md5</option>
1178 <option value="fastq_ftp">fastq_ftp</option>
1179 <option value="fastq_aspera">fastq_aspera</option>
1180 <option value="fastq_galaxy">fastq_galaxy</option>
1181 <option value="submitted_bytes">submitted_bytes</option>
1182 <option value="submitted_md5">submitted_md5</option>
1183 <option value="submitted_ftp">submitted_ftp</option>
1184 <option value="submitted_aspera">submitted_aspera</option>
1185 <option value="submitted_galaxy">submitted_galaxy</option>
1186 <option value="submitted_format">submitted_format</option>
1187 <option value="sra_bytes">sra_bytes</option>
1188 <option value="sra_md5">sra_md5</option>
1189 <option value="sra_ftp">sra_ftp</option>
1190 <option value="sra_aspera">sra_aspera</option>
1191 <option value="sra_galaxy">sra_galaxy</option>
1192 <option value="cram_index_ftp">cram_index_ftp</option>
1193 <option value="cram_index_aspera">cram_index_aspera</option>
1194 <option value="cram_index_galaxy">cram_index_galaxy</option>
1195 <option value="sample_alias">sample_alias</option>
1196 <option value="broker_name">broker_name</option>
1197 </param>
1198 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1199 <option value="secondary_sample_accession">secondary sample accession number</option>
1200 <option value="library_name">sequencing library name</option>
1201 <option value="read_count">number of reads</option>
1202 <option value="last_updated">date when last updated</option>
1203 <option value="center_name">Submitting center</option>
1204 <option value="submission_accession">submission accession number</option>
1205 <option value="nominal_length">average fragmentation size of paired reads</option>
1206 <option value="base_count">number of base pairs</option>
1207 <option value="run_accession">run accession number</option>
1208 <option value="library_selection">method used to select or enrich the material being sequenced</option>
1209 <option value="library_strategy">sequencing technique intended for the library</option>
1210 <option value="experiment_accession">experiment accession number</option>
1211 <option value="study_alias">submitter's name for the study</option>
1212 <option value="submitted_format"></option>
1213 <option value="broker_name">broker name</option>
1214 <option value="sample_alias">submitter's name for the sample</option>
1215 <option value="run_alias">submitter's name for the run</option>
1216 <option value="secondary_study_accession">project accession number</option>
1217 <option value="study_accession">study accession number</option>
1218 <option value="library_layout">sequencing library layout</option>
1219 <option value="library_source">source material being sequenced</option>
1220 <option value="experiment_title">brief experiment title</option>
1221 <option value="first_public">date when made public</option>
1222 <option value="instrument_platform">instrument platform used in sequencing experiment</option>
1223 <option value="instrument_model">instrument model used in sequencing experiment</option>
1224 <option value="sample_accession">sample accession number</option>
1225 <option value="experiment_alias">submitter's name for the experiment</option>
1226 <option value="study_title">brief sequencing study description</option>
1227 </param>
1228 </when>
1229 <when value="fasta"/>
1230 </conditional>
1231 </when>
1232 <when value="read_study">
1233 <conditional name="display_opt">
1234 <param argument="--display" type="select" label="Display option to specify the display format">
1235 <expand macro="display_options"/>
1236 </param>
1237 <when value="xml">
1238 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1239 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1240 </when>
1241 <when value="text">
1242 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1243 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1244 </when>
1245 <when value="fastq"/>
1246 <when value="html">
1247 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1248 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1249 </when>
1250 <when value="report">
1251 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1252 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1253 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1254 <option value="study_accession">study_accession</option>
1255 <option value="secondary_study_accession">secondary_study_accession</option>
1256 <option value="study_title">study_title</option>
1257 <option value="study_alias">study_alias</option>
1258 </param>
1259 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1260 <option value="study_title">brief sequencing study description</option>
1261 <option value="secondary_study_accession">project accession number</option>
1262 <option value="study_alias">submitter's name for the study</option>
1263 <option value="study_accession">study accession number</option>
1264 </param>
1265 </when>
1266 <when value="fasta"/>
1267 </conditional>
1268 </when>
1269 <when value="read_experiment">
1270 <conditional name="display_opt">
1271 <param argument="--display" type="select" label="Display option to specify the display format">
1272 <expand macro="display_options"/>
1273 </param>
1274 <when value="xml">
1275 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1276 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1277 </when>
1278 <when value="text">
1279 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1280 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1281 </when>
1282 <when value="fastq"/>
1283 <when value="html">
1284 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1285 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1286 </when>
1287 <when value="report">
1288 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1289 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1290 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1291 <option value="study_accession">study_accession</option>
1292 <option value="secondary_study_accession">secondary_study_accession</option>
1293 <option value="experiment_accession">experiment_accession</option>
1294 <option value="instrument_platform">instrument_platform</option>
1295 <option value="instrument_model">instrument_model</option>
1296 <option value="library_name">library_name</option>
1297 <option value="library_layout">library_layout</option>
1298 <option value="library_strategy">library_strategy</option>
1299 <option value="library_source">library_source</option>
1300 <option value="library_selection">library_selection</option>
1301 <option value="experiment_title">experiment_title</option>
1302 <option value="study_title">study_title</option>
1303 <option value="study_alias">study_alias</option>
1304 <option value="experiment_alias">experiment_alias</option>
1305 </param>
1306 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1307 <option value="library_name">sequencing library name</option>
1308 <option value="study_title">brief sequencing study description</option>
1309 <option value="instrument_platform">instrument platform used in sequencing experiment</option>
1310 <option value="instrument_model">instrument model used in sequencing experiment</option>
1311 <option value="study_alias">submitter's name for the study</option>
1312 <option value="experiment_alias">submitter's name for the experiment</option>
1313 <option value="secondary_study_accession">project accession number</option>
1314 <option value="study_accession">study accession number</option>
1315 <option value="library_selection">method used to select or enrich the material being sequenced</option>
1316 <option value="library_layout">sequencing library layout</option>
1317 <option value="library_strategy">sequencing technique intended for the library</option>
1318 <option value="experiment_accession">experiment accession number</option>
1319 <option value="library_source">source material being sequenced</option>
1320 <option value="experiment_title">brief experiment title</option>
1321 </param>
1322 </when>
1323 <when value="fasta"/>
1324 </conditional>
1325 </when>
1326 <when value="analysis">
1327 <conditional name="display_opt">
1328 <param argument="--display" type="select" label="Display option to specify the display format">
1329 <expand macro="display_options"/>
1330 </param>
1331 <when value="xml">
1332 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1333 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1334 </when>
1335 <when value="text">
1336 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1337 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1338 </when>
1339 <when value="fastq"/>
1340 <when value="html">
1341 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1342 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1343 </when>
1344 <when value="report">
1345 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1346 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1347 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1348 <option value="analysis_accession">analysis_accession</option>
1349 <option value="study_accession">study_accession</option>
1350 <option value="secondary_study_accession">secondary_study_accession</option>
1351 <option value="sample_accession">sample_accession</option>
1352 <option value="secondary_sample_accession">secondary_sample_accession</option>
1353 <option value="analysis_title">analysis_title</option>
1354 <option value="analysis_type">analysis_type</option>
1355 <option value="center_name">center_name</option>
1356 <option value="first_public">first_public</option>
1357 <option value="last_updated">last_updated</option>
1358 <option value="study_title">study_title</option>
1359 <option value="tax_id">tax_id</option>
1360 <option value="scientific_name">scientific_name</option>
1361 <option value="analysis_alias">analysis_alias</option>
1362 <option value="study_alias">study_alias</option>
1363 <option value="submitted_bytes">submitted_bytes</option>
1364 <option value="submitted_md5">submitted_md5</option>
1365 <option value="submitted_ftp">submitted_ftp</option>
1366 <option value="submitted_aspera">submitted_aspera</option>
1367 <option value="submitted_galaxy">submitted_galaxy</option>
1368 <option value="sample_alias">sample_alias</option>
1369 <option value="broker_name">broker_name</option>
1370 </param>
1371 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1372 <option value="secondary_sample_accession">secondary sample accession number</option>
1373 <option value="broker_name">broker name</option>
1374 <option value="study_accession">study accession number</option>
1375 <option value="last_updated">date when last updated</option>
1376 <option value="first_public">date when made public</option>
1377 <option value="sample_alias">submitter's name for the sample</option>
1378 <option value="center_name">Submitting center</option>
1379 <option value="analysis_title">brief sequence analysis description</option>
1380 <option value="sample_accession">sample accession number</option>
1381 <option value="analysis_accession">analysis accession number</option>
1382 <option value="secondary_study_accession">project accession number</option>
1383 <option value="analysis_alias">submitter's name for the analysis</option>
1384 <option value="analysis_type">type of sequence analysis</option>
1385 <option value="study_title">brief sequencing study description</option>
1386 <option value="study_alias">submitter's name for the study</option>
1387 </param>
1388 </when>
1389 <when value="fasta"/>
1390 </conditional>
1391 </when>
1392 <when value="sequence_update">
1393 <conditional name="display_opt">
1394 <param argument="--display" type="select" label="Display option to specify the display format">
1395 <expand macro="display_options"/>
1396 </param>
1397 <when value="xml">
1398 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1399 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1400 </when>
1401 <when value="text">
1402 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1403 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1404 </when>
1405 <when value="fastq"/>
1406 <when value="html">
1407 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1408 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1409 </when>
1410 <when value="report">
1411 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1412 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1413 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1414 <option value="accession">accession</option>
1415 <option value="base_count">base_count</option>
1416 <option value="bio_material">bio_material</option>
1417 <option value="cell_line">cell_line</option>
1418 <option value="cell_type">cell_type</option>
1419 <option value="collected_by">collected_by</option>
1420 <option value="collection_date">collection_date</option>
1421 <option value="country">country</option>
1422 <option value="cultivar">cultivar</option>
1423 <option value="culture_collection">culture_collection</option>
1424 <option value="dataclass">dataclass</option>
1425 <option value="description">description</option>
1426 <option value="dev_stage">dev_stage</option>
1427 <option value="ecotype">ecotype</option>
1428 <option value="environmental_sample">environmental_sample</option>
1429 <option value="first_public">first_public</option>
1430 <option value="germline">germline</option>
1431 <option value="host">host</option>
1432 <option value="identified_by">identified_by</option>
1433 <option value="isolate">isolate</option>
1434 <option value="isolation_source">isolation_source</option>
1435 <option value="keywords">keywords</option>
1436 <option value="lab_host">lab_host</option>
1437 <option value="last_updated">last_updated</option>
1438 <option value="location">location</option>
1439 <option value="mating_type">mating_type</option>
1440 <option value="mol_type">mol_type</option>
1441 <option value="organelle">organelle</option>
1442 <option value="serotype">serotype</option>
1443 <option value="serovar">serovar</option>
1444 <option value="sex">sex</option>
1445 <option value="submitted_sex">submitted_sex</option>
1446 <option value="specimen_voucher">specimen_voucher</option>
1447 <option value="strain">strain</option>
1448 <option value="sub_species">sub_species</option>
1449 <option value="sub_strain">sub_strain</option>
1450 <option value="tax_division">tax_division</option>
1451 <option value="tissue_lib">tissue_lib</option>
1452 <option value="tissue_type">tissue_type</option>
1453 <option value="topology">topology</option>
1454 <option value="variety">variety</option>
1455 <option value="tax_id">tax_id</option>
1456 <option value="scientific_name">scientific_name</option>
1457 <option value="altitude">altitude</option>
1458 <option value="haplotype">haplotype</option>
1459 <option value="plasmid">plasmid</option>
1460 <option value="study_accession">study_accession</option>
1461 <option value="sequence_md5">sequence_md5</option>
1462 </param>
1463 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1464 <option value="mol_type">in vivo molecule type of the sequence</option>
1465 <option value="last_updated">date when last updated</option>
1466 <option value="sequence_md5"></option>
1467 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
1468 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
1469 <option value="sex">sex of the organism from which the sample was obtained</option>
1470 <option value="keywords">keywords associated with sequence</option>
1471 <option value="collected_by">name of the person who collected the specimen</option>
1472 <option value="cell_line">cell line from which the sample was obtained</option>
1473 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
1474 <option value="bio_material">identifier for biological material including institute and collection code</option>
1475 <option value="identified_by">name of the taxonomist who identified the specimen</option>
1476 <option value="cell_type">cell type from which the sample was obtained</option>
1477 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
1478 <option value="tax_division">taxonomic division</option>
1479 <option value="collection_date">date that the specimen was collected</option>
1480 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
1481 <option value="altitude">Altitude (m)</option>
1482 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
1483 <option value="isolate">individual isolate from which sample was obtained</option>
1484 <option value="location">geographic location of isolation of the sample</option>
1485 <option value="study_accession">study accession number</option>
1486 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
1487 <option value="description">brief sequence description</option>
1488 <option value="accession">accession number</option>
1489 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
1490 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
1491 <option value="tissue_type">tissue type from which the sample was obtained</option>
1492 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
1493 <option value="tissue_lib">tissue library from which sample was obtained</option>
1494 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
1495 <option value="base_count">number of base pairs</option>
1496 <option value="topology">sequence topology: circular or linear</option>
1497 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
1498 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
1499 <option value="first_public">date when made public</option>
1500 <option value="strain">strain from which sample was obtained</option>
1501 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
1502 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
1503 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
1504 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
1505 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
1506 <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option>
1507 <option value="dataclass">sequence data class</option>
1508 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
1509 </param>
1510 </when>
1511 <when value="fasta"/>
1512 </conditional>
1513 </when>
1514 <when value="coding_update">
1515 <conditional name="display_opt">
1516 <param argument="--display" type="select" label="Display option to specify the display format">
1517 <expand macro="display_options"/>
1518 </param>
1519 <when value="xml">
1520 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1521 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1522 </when>
1523 <when value="text">
1524 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1525 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1526 </when>
1527 <when value="fastq"/>
1528 <when value="html">
1529 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1530 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1531 </when>
1532 <when value="report">
1533 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1534 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1535 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1536 <option value="accession">accession</option>
1537 <option value="base_count">base_count</option>
1538 <option value="bio_material">bio_material</option>
1539 <option value="cell_line">cell_line</option>
1540 <option value="cell_type">cell_type</option>
1541 <option value="collected_by">collected_by</option>
1542 <option value="collection_date">collection_date</option>
1543 <option value="country">country</option>
1544 <option value="cultivar">cultivar</option>
1545 <option value="culture_collection">culture_collection</option>
1546 <option value="dataclass">dataclass</option>
1547 <option value="description">description</option>
1548 <option value="dev_stage">dev_stage</option>
1549 <option value="ecotype">ecotype</option>
1550 <option value="environmental_sample">environmental_sample</option>
1551 <option value="first_public">first_public</option>
1552 <option value="germline">germline</option>
1553 <option value="host">host</option>
1554 <option value="identified_by">identified_by</option>
1555 <option value="isolate">isolate</option>
1556 <option value="isolation_source">isolation_source</option>
1557 <option value="keywords">keywords</option>
1558 <option value="lab_host">lab_host</option>
1559 <option value="last_updated">last_updated</option>
1560 <option value="location">location</option>
1561 <option value="mating_type">mating_type</option>
1562 <option value="mol_type">mol_type</option>
1563 <option value="organelle">organelle</option>
1564 <option value="serotype">serotype</option>
1565 <option value="serovar">serovar</option>
1566 <option value="sex">sex</option>
1567 <option value="submitted_sex">submitted_sex</option>
1568 <option value="specimen_voucher">specimen_voucher</option>
1569 <option value="strain">strain</option>
1570 <option value="sub_species">sub_species</option>
1571 <option value="sub_strain">sub_strain</option>
1572 <option value="tax_division">tax_division</option>
1573 <option value="tissue_lib">tissue_lib</option>
1574 <option value="tissue_type">tissue_type</option>
1575 <option value="variety">variety</option>
1576 <option value="allele">allele</option>
1577 <option value="artificial_location">artificial_location</option>
1578 <option value="codon_start">codon_start</option>
1579 <option value="ec_number">ec_number</option>
1580 <option value="exception">exception</option>
1581 <option value="experiment">experiment</option>
1582 <option value="function">function</option>
1583 <option value="topology">topology</option>
1584 <option value="gene">gene</option>
1585 <option value="gene_synonym">gene_synonym</option>
1586 <option value="inference">inference</option>
1587 <option value="locus_tag">locus_tag</option>
1588 <option value="map">map</option>
1589 <option value="note">note</option>
1590 <option value="old_locus_tag">old_locus_tag</option>
1591 <option value="operon">operon</option>
1592 <option value="partial">partial</option>
1593 <option value="product">product</option>
1594 <option value="protein_id">protein_id</option>
1595 <option value="pseudo">pseudo</option>
1596 <option value="pseudo_gene">pseudo_gene</option>
1597 <option value="ribosomal_slippage">ribosomal_slippage</option>
1598 <option value="standard_name">standard_name</option>
1599 <option value="trans_splicing">trans_splicing</option>
1600 <option value="transl_except">transl_except</option>
1601 <option value="transl_table">transl_table</option>
1602 <option value="tax_id">tax_id</option>
1603 <option value="scientific_name">scientific_name</option>
1604 <option value="parent_accession">parent_accession</option>
1605 <option value="altitude">altitude</option>
1606 <option value="haplotype">haplotype</option>
1607 <option value="sequence_md5">sequence_md5</option>
1608 </param>
1609 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1610 <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option>
1611 <option value="mol_type">in vivo molecule type of the sequence</option>
1612 <option value="last_updated">date when last updated</option>
1613 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
1614 <option value="transl_except">a single codon translation that does not conform to genetic code</option>
1615 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
1616 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
1617 <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option>
1618 <option value="sex">sex of the organism from which the sample was obtained</option>
1619 <option value="pseudo_gene">indicates that this feature is a pseudogene</option>
1620 <option value="standard_name">accepted standard name for a feature</option>
1621 <option value="collected_by">name of the person who collected the specimen</option>
1622 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
1623 <option value="cell_type">cell type from which the sample was obtained</option>
1624 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
1625 <option value="inference">a structured description of non-experimental evidence</option>
1626 <option value="bio_material">identifier for biological material including institute and collection code</option>
1627 <option value="parent_accession">parent sequence accession number</option>
1628 <option value="identified_by">name of the taxonomist who identified the specimen</option>
1629 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
1630 <option value="sequence_md5"></option>
1631 <option value="tax_division">taxonomic division</option>
1632 <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
1633 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
1634 <option value="altitude">Altitude (m)</option>
1635 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
1636 <option value="isolate">individual isolate from which sample was obtained</option>
1637 <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option>
1638 <option value="note">any comment or additional information</option>
1639 <option value="experiment">a brief description of the nature of the experimental evidence</option>
1640 <option value="location">geographic location of isolation of the sample</option>
1641 <option value="collection_date">date that the specimen was collected</option>
1642 <option value="allele">name of the allele for the given gene</option>
1643 <option value="protein_id">a stable protein identifier issued by INSDC</option>
1644 <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option>
1645 <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option>
1646 <option value="function">function attributed to a sequence</option>
1647 <option value="map">genomic map position of feature</option>
1648 <option value="product">name of the product associated with the feature</option>
1649 <option value="description">brief sequence description</option>
1650 <option value="cell_line">cell line from which the sample was obtained</option>
1651 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
1652 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
1653 <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option>
1654 <option value="accession">accession number</option>
1655 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
1656 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
1657 <option value="tissue_type">tissue type from which the sample was obtained</option>
1658 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
1659 <option value="tissue_lib">tissue library from which sample was obtained</option>
1660 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
1661 <option value="base_count">number of base pairs</option>
1662 <option value="topology">sequence topology: circular or linear</option>
1663 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
1664 <option value="first_public">date when made public</option>
1665 <option value="strain">strain from which sample was obtained</option>
1666 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
1667 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
1668 <option value="pseudo">the feature is non-functional</option>
1669 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
1670 <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option>
1671 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
1672 <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option>
1673 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
1674 <option value="keywords">keywords associated with sequence</option>
1675 <option value="dataclass">sequence data class</option>
1676 <option value="gene">symbol of the gene corresponding to a sequence region</option>
1677 <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option>
1678 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
1679 </param>
1680 </when>
1681 <when value="fasta"/>
1682 </conditional>
1683 </when>
1684 <when value="tsa_set">
1685 <conditional name="display_opt">
1686 <param argument="--display" type="select" label="Display option to specify the display format">
1687 <expand macro="display_options"/>
1688 </param>
1689 <when value="xml">
1690 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1691 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1692 </when>
1693 <when value="text">
1694 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1695 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1696 </when>
1697 <when value="fastq"/>
1698 <when value="html">
1699 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1700 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1701 </when>
1702 <when value="report">
1703 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1704 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1705 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1706 <option value="accession">accession</option>
1707 <option value="bio_material">bio_material</option>
1708 <option value="cell_line">cell_line</option>
1709 <option value="cell_type">cell_type</option>
1710 <option value="collected_by">collected_by</option>
1711 <option value="collection_date">collection_date</option>
1712 <option value="country">country</option>
1713 <option value="cultivar">cultivar</option>
1714 <option value="culture_collection">culture_collection</option>
1715 <option value="description">description</option>
1716 <option value="dev_stage">dev_stage</option>
1717 <option value="ecotype">ecotype</option>
1718 <option value="environmental_sample">environmental_sample</option>
1719 <option value="first_public">first_public</option>
1720 <option value="germline">germline</option>
1721 <option value="host">host</option>
1722 <option value="identified_by">identified_by</option>
1723 <option value="isolate">isolate</option>
1724 <option value="isolation_source">isolation_source</option>
1725 <option value="keywords">keywords</option>
1726 <option value="lab_host">lab_host</option>
1727 <option value="last_updated">last_updated</option>
1728 <option value="location">location</option>
1729 <option value="mating_type">mating_type</option>
1730 <option value="mol_type">mol_type</option>
1731 <option value="serotype">serotype</option>
1732 <option value="serovar">serovar</option>
1733 <option value="sex">sex</option>
1734 <option value="submitted_sex">submitted_sex</option>
1735 <option value="specimen_voucher">specimen_voucher</option>
1736 <option value="strain">strain</option>
1737 <option value="sub_species">sub_species</option>
1738 <option value="sub_strain">sub_strain</option>
1739 <option value="tax_division">tax_division</option>
1740 <option value="tissue_lib">tissue_lib</option>
1741 <option value="tissue_type">tissue_type</option>
1742 <option value="variety">variety</option>
1743 <option value="tax_id">tax_id</option>
1744 <option value="scientific_name">scientific_name</option>
1745 <option value="altitude">altitude</option>
1746 <option value="haplotype">haplotype</option>
1747 <option value="study_accession">study_accession</option>
1748 <option value="set_files">set_files</option>
1749 </param>
1750 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1751 <option value="mol_type">in vivo molecule type of the sequence</option>
1752 <option value="last_updated">date when last updated</option>
1753 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
1754 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
1755 <option value="accession">accession number</option>
1756 <option value="sex">sex of the organism from which the sample was obtained</option>
1757 <option value="cell_line">cell line from which the sample was obtained</option>
1758 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
1759 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
1760 <option value="bio_material">identifier for biological material including institute and collection code</option>
1761 <option value="identified_by">name of the taxonomist who identified the specimen</option>
1762 <option value="cell_type">cell type from which the sample was obtained</option>
1763 <option value="tax_division">taxonomic division</option>
1764 <option value="collection_date">date that the specimen was collected</option>
1765 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
1766 <option value="altitude">Altitude (m)</option>
1767 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
1768 <option value="isolate">individual isolate from which sample was obtained</option>
1769 <option value="location">geographic location of isolation of the sample</option>
1770 <option value="study_accession">study accession number</option>
1771 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
1772 <option value="description">brief sequence description</option>
1773 <option value="tissue_lib">tissue library from which sample was obtained</option>
1774 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
1775 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
1776 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
1777 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
1778 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
1779 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
1780 <option value="collected_by">name of the person who collected the specimen</option>
1781 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
1782 <option value="first_public">date when made public</option>
1783 <option value="strain">strain from which sample was obtained</option>
1784 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
1785 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
1786 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
1787 <option value="tissue_type">tissue type from which the sample was obtained</option>
1788 <option value="keywords">keywords associated with sequence</option>
1789 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
1790 </param>
1791 </when>
1792 <when value="fasta"/>
1793 </conditional>
1794 </when>
1795 <when value="analysis_study">
1796 <conditional name="display_opt">
1797 <param argument="--display" type="select" label="Display option to specify the display format">
1798 <expand macro="display_options"/>
1799 </param>
1800 <when value="xml">
1801 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1802 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1803 </when>
1804 <when value="text">
1805 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1806 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1807 </when>
1808 <when value="fastq"/>
1809 <when value="html">
1810 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1811 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1812 </when>
1813 <when value="report">
1814 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1815 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1816 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1817 <option value="study_accession">study_accession</option>
1818 <option value="secondary_study_accession">secondary_study_accession</option>
1819 <option value="study_title">study_title</option>
1820 <option value="study_alias">study_alias</option>
1821 </param>
1822 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1823 <option value="study_title">brief sequencing study description</option>
1824 <option value="secondary_study_accession">project accession number</option>
1825 <option value="study_alias">submitter's name for the study</option>
1826 <option value="study_accession">study accession number</option>
1827 </param>
1828 </when>
1829 <when value="fasta"/>
1830 </conditional>
1831 </when>
1832 <when value="noncoding_update">
1833 <conditional name="display_opt">
1834 <param argument="--display" type="select" label="Display option to specify the display format">
1835 <expand macro="display_options"/>
1836 </param>
1837 <when value="xml">
1838 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1839 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1840 </when>
1841 <when value="text">
1842 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1843 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1844 </when>
1845 <when value="fastq"/>
1846 <when value="html">
1847 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1848 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1849 </when>
1850 <when value="report">
1851 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
1852 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
1853 <param argument="--fields" type="select" multiple="true" label="Fields to return">
1854 <option value="accession">accession</option>
1855 <option value="base_count">base_count</option>
1856 <option value="collected_by">collected_by</option>
1857 <option value="dataclass">dataclass</option>
1858 <option value="first_public">first_public</option>
1859 <option value="last_updated">last_updated</option>
1860 <option value="location">location</option>
1861 <option value="tax_division">tax_division</option>
1862 <option value="tax_id">tax_id</option>
1863 <option value="scientific_name">scientific_name</option>
1864 <option value="rna_class">rna_class</option>
1865 <option value="gene">gene</option>
1866 <option value="gene_synonym">gene_synonym</option>
1867 <option value="product">product</option>
1868 <option value="anticodon">anticodon</option>
1869 <option value="function">function</option>
1870 <option value="locus_tag">locus_tag</option>
1871 <option value="experiment">experiment</option>
1872 <option value="inference">inference</option>
1873 <option value="note">note</option>
1874 <option value="bio_material">bio_material</option>
1875 <option value="cell_line">cell_line</option>
1876 <option value="cell_type">cell_type</option>
1877 <option value="country">country</option>
1878 <option value="cultivar">cultivar</option>
1879 <option value="culture_collection">culture_collection</option>
1880 <option value="description">description</option>
1881 <option value="dev_stage">dev_stage</option>
1882 <option value="ecotype">ecotype</option>
1883 <option value="environmental_sample">environmental_sample</option>
1884 <option value="germline">germline</option>
1885 <option value="host">host</option>
1886 <option value="identified_by">identified_by</option>
1887 <option value="isolate">isolate</option>
1888 <option value="isolation_source">isolation_source</option>
1889 <option value="keywords">keywords</option>
1890 <option value="lab_host">lab_host</option>
1891 <option value="mating_type">mating_type</option>
1892 <option value="mol_type">mol_type</option>
1893 <option value="organelle">organelle</option>
1894 <option value="serotype">serotype</option>
1895 <option value="serovar">serovar</option>
1896 <option value="sex">sex</option>
1897 <option value="collection_date">collection_date</option>
1898 <option value="submitted_sex">submitted_sex</option>
1899 <option value="specimen_voucher">specimen_voucher</option>
1900 <option value="strain">strain</option>
1901 <option value="sub_species">sub_species</option>
1902 <option value="sub_strain">sub_strain</option>
1903 <option value="tissue_lib">tissue_lib</option>
1904 <option value="tissue_type">tissue_type</option>
1905 <option value="topology">topology</option>
1906 <option value="variety">variety</option>
1907 <option value="sequence_md5">sequence_md5</option>
1908 <option value="study_accession">study_accession</option>
1909 </param>
1910 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
1911 <option value="mol_type">in vivo molecule type of the sequence</option>
1912 <option value="last_updated">date when last updated</option>
1913 <option value="sequence_md5"></option>
1914 <option value="collected_by">name of the person who collected the specimen</option>
1915 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
1916 <option value="sex">sex of the organism from which the sample was obtained</option>
1917 <option value="keywords">keywords associated with sequence</option>
1918 <option value="cell_line">cell line from which the sample was obtained</option>
1919 <option value="inference">a structured description of non-experimental evidence</option>
1920 <option value="bio_material">identifier for biological material including institute and collection code</option>
1921 <option value="identified_by">name of the taxonomist who identified the specimen</option>
1922 <option value="note">any comment or additional information</option>
1923 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
1924 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
1925 <option value="tax_division">taxonomic division</option>
1926 <option value="collection_date">date that the specimen was collected</option>
1927 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
1928 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
1929 <option value="isolate">individual isolate from which sample was obtained</option>
1930 <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option>
1931 <option value="experiment">a brief description of the nature of the experimental evidence</option>
1932 <option value="location">geographic location of isolation of the sample</option>
1933 <option value="study_accession">study accession number</option>
1934 <option value="function">function attributed to a sequence</option>
1935 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
1936 <option value="product">name of the product associated with the feature</option>
1937 <option value="description">brief sequence description</option>
1938 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
1939 <option value="cell_type">cell type from which the sample was obtained</option>
1940 <option value="accession">accession number</option>
1941 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
1942 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
1943 <option value="tissue_type">tissue type from which the sample was obtained</option>
1944 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
1945 <option value="tissue_lib">tissue library from which sample was obtained</option>
1946 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
1947 <option value="base_count">number of base pairs</option>
1948 <option value="topology">sequence topology: circular or linear</option>
1949 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
1950 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
1951 <option value="first_public">date when made public</option>
1952 <option value="strain">strain from which sample was obtained</option>
1953 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
1954 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
1955 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
1956 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
1957 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
1958 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
1959 <option value="rna_class">classification of RNA</option>
1960 <option value="dataclass">sequence data class</option>
1961 <option value="gene">symbol of the gene corresponding to a sequence region</option>
1962 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
1963 </param>
1964 </when>
1965 <when value="fasta"/>
1966 </conditional>
1967 </when>
1968 </conditional>
1969 </xml>
1970 <xml name="conditional_text_search">
1971 <conditional name="res">
1972 <param argument="--result" type="select" label="Result to return">
1973 <option value="noncoding_release">Non-coding sequences (Release)</option>
1974 <option value="assembly">Genome assemblies</option>
1975 <option value="sequence_release">Nucleotide sequences (Release)</option>
1976 <option value="wgs_set">Genome assembly contig set</option>
1977 <option value="study">Studies</option>
1978 <option value="taxon">Taxonomic classification</option>
1979 <option value="coding_release">Protein-coding sequences (Release)</option>
1980 <option value="sample">Samples</option>
1981 <option value="environmental">Environmental samples</option>
1982 <option value="read_run">Raw reads</option>
1983 <option value="read_study">Raw reads (grouped by study)</option>
1984 <option value="read_experiment">Raw reads (grouped by experiment)</option>
1985 <option value="analysis">Nucleotide sequence analyses from reads</option>
1986 <option value="sequence_update">Nucleotide sequences (Update)</option>
1987 <option value="coding_update">Protein-coding sequences (Update)</option>
1988 <option value="tsa_set">Transcriptome assembly contig set</option>
1989 <option value="analysis_study">Nucleotide sequence analyses from reads (grouped by study)</option>
1990 <option value="noncoding_update">Non-coding sequences (Update)</option>
1991 </param>
1992 <when value="noncoding_release">
1993 <repeat name="queries" title="Add a query">
1994 <param name="combination_operation" type="select" label="Combination operation">
1995 <option value="AND">AND</option>
1996 <option value="OR">OR</option>
1997 <option value="NOT">NOT</option>
1998 </param>
1999 <conditional name="filter_field">
2000 <param name="field" type="select" label="Field to query">
2001 <option value="mol_type">in vivo molecule type of the sequence</option>
2002 <option value="last_updated">date when last updated</option>
2003 <option value="sequence_md5"></option>
2004 <option value="collected_by">name of the person who collected the specimen</option>
2005 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
2006 <option value="sex">sex of the organism from which the sample was obtained</option>
2007 <option value="keywords">keywords associated with sequence</option>
2008 <option value="cell_line">cell line from which the sample was obtained</option>
2009 <option value="inference">a structured description of non-experimental evidence</option>
2010 <option value="bio_material">identifier for biological material including institute and collection code</option>
2011 <option value="identified_by">name of the taxonomist who identified the specimen</option>
2012 <option value="note">any comment or additional information</option>
2013 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
2014 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
2015 <option value="tax_division">taxonomic division</option>
2016 <option value="collection_date">date that the specimen was collected</option>
2017 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
2018 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
2019 <option value="isolate">individual isolate from which sample was obtained</option>
2020 <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option>
2021 <option value="experiment">a brief description of the nature of the experimental evidence</option>
2022 <option value="location">geographic location of isolation of the sample</option>
2023 <option value="study_accession">study accession number</option>
2024 <option value="function">function attributed to a sequence</option>
2025 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
2026 <option value="product">name of the product associated with the feature</option>
2027 <option value="description">brief sequence description</option>
2028 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
2029 <option value="cell_type">cell type from which the sample was obtained</option>
2030 <option value="accession">accession number</option>
2031 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
2032 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
2033 <option value="tissue_type">tissue type from which the sample was obtained</option>
2034 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
2035 <option value="tissue_lib">tissue library from which sample was obtained</option>
2036 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
2037 <option value="base_count">number of base pairs</option>
2038 <option value="topology">sequence topology: circular or linear</option>
2039 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
2040 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
2041 <option value="first_public">date when made public</option>
2042 <option value="strain">strain from which sample was obtained</option>
2043 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
2044 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
2045 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
2046 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
2047 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
2048 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
2049 <option value="rna_class">classification of RNA</option>
2050 <option value="dataclass">sequence data class</option>
2051 <option value="gene">symbol of the gene corresponding to a sequence region</option>
2052 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
2053 </param>
2054 <when value="mol_type">
2055 <param name="operation" type="select" label="Operator">
2056 <option value="equal">equal</option>
2057 <option value="different">different</option>
2058 </param>
2059 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2060 </when>
2061 <when value="last_updated">
2062 <param name="operation" type="select" label="Operator">
2063 <option value="equal">equal</option>
2064 <option value="different">different</option>
2065 <option value="lower">lower</option>
2066 <option value="equal or lower">equal or lower</option>
2067 <option value="higher">higher</option>
2068 <option value="equal or higher">equal or higher</option>
2069 </param>
2070 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
2071 </when>
2072 <when value="sequence_md5">
2073 <param name="operation" type="select" label="Operator">
2074 <option value="equal">equal</option>
2075 <option value="different">different</option>
2076 </param>
2077 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2078 </when>
2079 <when value="collected_by">
2080 <param name="operation" type="select" label="Operator">
2081 <option value="equal">equal</option>
2082 <option value="different">different</option>
2083 </param>
2084 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2085 </when>
2086 <when value="serotype">
2087 <param name="operation" type="select" label="Operator">
2088 <option value="equal">equal</option>
2089 <option value="different">different</option>
2090 </param>
2091 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2092 </when>
2093 <when value="sex">
2094 <param name="operation" type="select" label="Operator">
2095 <option value="equal">equal</option>
2096 <option value="different">different</option>
2097 </param>
2098 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2099 </when>
2100 <when value="keywords">
2101 <param name="operation" type="select" label="Operator">
2102 <option value="equal">equal</option>
2103 <option value="different">different</option>
2104 </param>
2105 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2106 </when>
2107 <when value="cell_line">
2108 <param name="operation" type="select" label="Operator">
2109 <option value="equal">equal</option>
2110 <option value="different">different</option>
2111 </param>
2112 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2113 </when>
2114 <when value="inference">
2115 <param name="operation" type="select" label="Operator">
2116 <option value="equal">equal</option>
2117 <option value="different">different</option>
2118 </param>
2119 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2120 </when>
2121 <when value="bio_material">
2122 <param name="operation" type="select" label="Operator">
2123 <option value="equal">equal</option>
2124 <option value="different">different</option>
2125 </param>
2126 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2127 </when>
2128 <when value="identified_by">
2129 <param name="operation" type="select" label="Operator">
2130 <option value="equal">equal</option>
2131 <option value="different">different</option>
2132 </param>
2133 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2134 </when>
2135 <when value="note">
2136 <param name="operation" type="select" label="Operator">
2137 <option value="equal">equal</option>
2138 <option value="different">different</option>
2139 </param>
2140 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2141 </when>
2142 <when value="locus_tag">
2143 <param name="operation" type="select" label="Operator">
2144 <option value="equal">equal</option>
2145 <option value="different">different</option>
2146 </param>
2147 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2148 </when>
2149 <when value="lab_host">
2150 <param name="operation" type="select" label="Operator">
2151 <option value="equal">equal</option>
2152 <option value="different">different</option>
2153 </param>
2154 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2155 </when>
2156 <when value="tax_division">
2157 <param name="operation" type="select" label="Operator">
2158 <option value="equal">equal</option>
2159 <option value="different">different</option>
2160 </param>
2161 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2162 </when>
2163 <when value="collection_date">
2164 <param name="operation" type="select" label="Operator">
2165 <option value="equal">equal</option>
2166 <option value="different">different</option>
2167 <option value="lower">lower</option>
2168 <option value="equal or lower">equal or lower</option>
2169 <option value="higher">higher</option>
2170 <option value="equal or higher">equal or higher</option>
2171 </param>
2172 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
2173 </when>
2174 <when value="specimen_voucher">
2175 <param name="operation" type="select" label="Operator">
2176 <option value="equal">equal</option>
2177 <option value="different">different</option>
2178 </param>
2179 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2180 </when>
2181 <when value="dev_stage">
2182 <param name="operation" type="select" label="Operator">
2183 <option value="equal">equal</option>
2184 <option value="different">different</option>
2185 </param>
2186 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2187 </when>
2188 <when value="isolate">
2189 <param name="operation" type="select" label="Operator">
2190 <option value="equal">equal</option>
2191 <option value="different">different</option>
2192 </param>
2193 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2194 </when>
2195 <when value="anticodon">
2196 <param name="operation" type="select" label="Operator">
2197 <option value="equal">equal</option>
2198 <option value="different">different</option>
2199 </param>
2200 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2201 </when>
2202 <when value="experiment">
2203 <param name="operation" type="select" label="Operator">
2204 <option value="equal">equal</option>
2205 <option value="different">different</option>
2206 </param>
2207 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2208 </when>
2209 <when value="location">
2210 <conditional name="op">
2211 <param name="operation" type="select" label="Operation">
2212 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
2213 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
2214 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
2215 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
2216 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
2217 <option value="geo_point">An exact lat/lon position</option>
2218 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
2219 </param>
2220 <when value="geo_box2">
2221 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
2222 </when>
2223 <when value="geo_box1">
2224 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
2225 </when>
2226 <when value="geo_circ">
2227 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
2228 </when>
2229 <when value="geo_lat">
2230 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
2231 </when>
2232 <when value="geo_south">
2233 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
2234 </when>
2235 <when value="geo_point">
2236 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
2237 </when>
2238 <when value="geo_north">
2239 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
2240 </when>
2241 </conditional>
2242 </when>
2243 <when value="study_accession">
2244 <param name="operation" type="select" label="Operator">
2245 <option value="equal">equal</option>
2246 <option value="different">different</option>
2247 </param>
2248 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2249 </when>
2250 <when value="function">
2251 <param name="operation" type="select" label="Operator">
2252 <option value="equal">equal</option>
2253 <option value="different">different</option>
2254 </param>
2255 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2256 </when>
2257 <when value="germline">
2258 <param name="operation" type="select" label="Operator">
2259 <option value="equal">equal</option>
2260 </param>
2261 <param name="value" type="select" label="Value">
2262 <option value="yes">yes</option>
2263 <option value="true">true</option>
2264 <option value="no">no</option>
2265 <option value="false">false</option>
2266 </param>
2267 </when>
2268 <when value="product">
2269 <param name="operation" type="select" label="Operator">
2270 <option value="equal">equal</option>
2271 <option value="different">different</option>
2272 </param>
2273 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2274 </when>
2275 <when value="description">
2276 <param name="operation" type="select" label="Operator">
2277 <option value="equal">equal</option>
2278 <option value="different">different</option>
2279 </param>
2280 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2281 </when>
2282 <when value="ecotype">
2283 <param name="operation" type="select" label="Operator">
2284 <option value="equal">equal</option>
2285 <option value="different">different</option>
2286 </param>
2287 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2288 </when>
2289 <when value="cell_type">
2290 <param name="operation" type="select" label="Operator">
2291 <option value="equal">equal</option>
2292 <option value="different">different</option>
2293 </param>
2294 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2295 </when>
2296 <when value="accession">
2297 <param name="operation" type="select" label="Operator">
2298 <option value="equal">equal</option>
2299 <option value="different">different</option>
2300 </param>
2301 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2302 </when>
2303 <when value="isolation_source">
2304 <param name="operation" type="select" label="Operator">
2305 <option value="equal">equal</option>
2306 <option value="different">different</option>
2307 </param>
2308 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2309 </when>
2310 <when value="mating_type">
2311 <param name="operation" type="select" label="Operator">
2312 <option value="equal">equal</option>
2313 <option value="different">different</option>
2314 </param>
2315 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2316 </when>
2317 <when value="tissue_type">
2318 <param name="operation" type="select" label="Operator">
2319 <option value="equal">equal</option>
2320 <option value="different">different</option>
2321 </param>
2322 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2323 </when>
2324 <when value="sub_strain">
2325 <param name="operation" type="select" label="Operator">
2326 <option value="equal">equal</option>
2327 <option value="different">different</option>
2328 </param>
2329 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2330 </when>
2331 <when value="tissue_lib">
2332 <param name="operation" type="select" label="Operator">
2333 <option value="equal">equal</option>
2334 <option value="different">different</option>
2335 </param>
2336 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2337 </when>
2338 <when value="cultivar">
2339 <param name="operation" type="select" label="Operator">
2340 <option value="equal">equal</option>
2341 <option value="different">different</option>
2342 </param>
2343 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2344 </when>
2345 <when value="base_count">
2346 <param name="operation" type="select" label="Operator">
2347 <option value="equal">equal</option>
2348 <option value="different">different</option>
2349 <option value="lower">lower</option>
2350 <option value="equal or lower">equal or lower</option>
2351 <option value="higher">higher</option>
2352 <option value="equal or higher">equal or higher</option>
2353 </param>
2354 <param name="value" type="float" value="" label="Any integer"/>
2355 </when>
2356 <when value="topology">
2357 <param name="operation" type="select" label="Operator">
2358 <option value="equal">equal</option>
2359 <option value="different">different</option>
2360 </param>
2361 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2362 </when>
2363 <when value="sub_species">
2364 <param name="operation" type="select" label="Operator">
2365 <option value="equal">equal</option>
2366 <option value="different">different</option>
2367 </param>
2368 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2369 </when>
2370 <when value="environmental_sample">
2371 <param name="operation" type="select" label="Operator">
2372 <option value="equal">equal</option>
2373 </param>
2374 <param name="value" type="select" label="Value">
2375 <option value="yes">yes</option>
2376 <option value="true">true</option>
2377 <option value="no">no</option>
2378 <option value="false">false</option>
2379 </param>
2380 </when>
2381 <when value="first_public">
2382 <param name="operation" type="select" label="Operator">
2383 <option value="equal">equal</option>
2384 <option value="different">different</option>
2385 <option value="lower">lower</option>
2386 <option value="equal or lower">equal or lower</option>
2387 <option value="higher">higher</option>
2388 <option value="equal or higher">equal or higher</option>
2389 </param>
2390 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
2391 </when>
2392 <when value="strain">
2393 <param name="operation" type="select" label="Operator">
2394 <option value="equal">equal</option>
2395 <option value="different">different</option>
2396 </param>
2397 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2398 </when>
2399 <when value="country">
2400 <param name="operation" type="select" label="Operator">
2401 <option value="equal">equal</option>
2402 <option value="different">different</option>
2403 </param>
2404 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2405 </when>
2406 <when value="variety">
2407 <param name="operation" type="select" label="Operator">
2408 <option value="equal">equal</option>
2409 <option value="different">different</option>
2410 </param>
2411 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2412 </when>
2413 <when value="host">
2414 <param name="operation" type="select" label="Operator">
2415 <option value="equal">equal</option>
2416 <option value="different">different</option>
2417 </param>
2418 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2419 </when>
2420 <when value="gene_synonym">
2421 <param name="operation" type="select" label="Operator">
2422 <option value="equal">equal</option>
2423 <option value="different">different</option>
2424 </param>
2425 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2426 </when>
2427 <when value="organelle">
2428 <param name="operation" type="select" label="Operator">
2429 <option value="equal">equal</option>
2430 <option value="different">different</option>
2431 </param>
2432 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2433 </when>
2434 <when value="serovar">
2435 <param name="operation" type="select" label="Operator">
2436 <option value="equal">equal</option>
2437 <option value="different">different</option>
2438 </param>
2439 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2440 </when>
2441 <when value="rna_class">
2442 <param name="operation" type="select" label="Operator">
2443 <option value="equal">equal</option>
2444 <option value="different">different</option>
2445 </param>
2446 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2447 </when>
2448 <when value="dataclass">
2449 <param name="operation" type="select" label="Operator">
2450 <option value="equal">equal</option>
2451 <option value="different">different</option>
2452 </param>
2453 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2454 </when>
2455 <when value="gene">
2456 <param name="operation" type="select" label="Operator">
2457 <option value="equal">equal</option>
2458 <option value="different">different</option>
2459 </param>
2460 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2461 </when>
2462 <when value="culture_collection">
2463 <param name="operation" type="select" label="Operator">
2464 <option value="equal">equal</option>
2465 <option value="different">different</option>
2466 </param>
2467 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2468 </when>
2469 </conditional>
2470 </repeat>
2471 <conditional name="display_opt">
2472 <param argument="--display" type="select" label="Display option to specify the display format">
2473 <expand macro="display_options"/>
2474 </param>
2475 <when value="xml">
2476 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2477 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2478 </when>
2479 <when value="text">
2480 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2481 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2482 </when>
2483 <when value="fastq"/>
2484 <when value="html">
2485 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2486 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2487 </when>
2488 <when value="report">
2489 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2490 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2491 <param argument="--fields" type="select" multiple="true" label="Fields to return">
2492 <option value="accession">accession</option>
2493 <option value="base_count">base_count</option>
2494 <option value="collected_by">collected_by</option>
2495 <option value="dataclass">dataclass</option>
2496 <option value="first_public">first_public</option>
2497 <option value="last_updated">last_updated</option>
2498 <option value="location">location</option>
2499 <option value="tax_division">tax_division</option>
2500 <option value="tax_id">tax_id</option>
2501 <option value="scientific_name">scientific_name</option>
2502 <option value="rna_class">rna_class</option>
2503 <option value="gene">gene</option>
2504 <option value="gene_synonym">gene_synonym</option>
2505 <option value="product">product</option>
2506 <option value="anticodon">anticodon</option>
2507 <option value="function">function</option>
2508 <option value="locus_tag">locus_tag</option>
2509 <option value="experiment">experiment</option>
2510 <option value="inference">inference</option>
2511 <option value="note">note</option>
2512 <option value="bio_material">bio_material</option>
2513 <option value="cell_line">cell_line</option>
2514 <option value="cell_type">cell_type</option>
2515 <option value="country">country</option>
2516 <option value="cultivar">cultivar</option>
2517 <option value="culture_collection">culture_collection</option>
2518 <option value="description">description</option>
2519 <option value="dev_stage">dev_stage</option>
2520 <option value="ecotype">ecotype</option>
2521 <option value="environmental_sample">environmental_sample</option>
2522 <option value="germline">germline</option>
2523 <option value="host">host</option>
2524 <option value="identified_by">identified_by</option>
2525 <option value="isolate">isolate</option>
2526 <option value="isolation_source">isolation_source</option>
2527 <option value="keywords">keywords</option>
2528 <option value="lab_host">lab_host</option>
2529 <option value="mating_type">mating_type</option>
2530 <option value="mol_type">mol_type</option>
2531 <option value="organelle">organelle</option>
2532 <option value="serotype">serotype</option>
2533 <option value="serovar">serovar</option>
2534 <option value="sex">sex</option>
2535 <option value="collection_date">collection_date</option>
2536 <option value="submitted_sex">submitted_sex</option>
2537 <option value="specimen_voucher">specimen_voucher</option>
2538 <option value="strain">strain</option>
2539 <option value="sub_species">sub_species</option>
2540 <option value="sub_strain">sub_strain</option>
2541 <option value="tissue_lib">tissue_lib</option>
2542 <option value="tissue_type">tissue_type</option>
2543 <option value="topology">topology</option>
2544 <option value="variety">variety</option>
2545 <option value="sequence_md5">sequence_md5</option>
2546 <option value="study_accession">study_accession</option>
2547 </param>
2548 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
2549 <option value="mol_type">in vivo molecule type of the sequence</option>
2550 <option value="last_updated">date when last updated</option>
2551 <option value="sequence_md5"></option>
2552 <option value="collected_by">name of the person who collected the specimen</option>
2553 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
2554 <option value="sex">sex of the organism from which the sample was obtained</option>
2555 <option value="keywords">keywords associated with sequence</option>
2556 <option value="cell_line">cell line from which the sample was obtained</option>
2557 <option value="inference">a structured description of non-experimental evidence</option>
2558 <option value="bio_material">identifier for biological material including institute and collection code</option>
2559 <option value="identified_by">name of the taxonomist who identified the specimen</option>
2560 <option value="note">any comment or additional information</option>
2561 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
2562 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
2563 <option value="tax_division">taxonomic division</option>
2564 <option value="collection_date">date that the specimen was collected</option>
2565 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
2566 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
2567 <option value="isolate">individual isolate from which sample was obtained</option>
2568 <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option>
2569 <option value="experiment">a brief description of the nature of the experimental evidence</option>
2570 <option value="location">geographic location of isolation of the sample</option>
2571 <option value="study_accession">study accession number</option>
2572 <option value="function">function attributed to a sequence</option>
2573 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
2574 <option value="product">name of the product associated with the feature</option>
2575 <option value="description">brief sequence description</option>
2576 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
2577 <option value="cell_type">cell type from which the sample was obtained</option>
2578 <option value="accession">accession number</option>
2579 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
2580 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
2581 <option value="tissue_type">tissue type from which the sample was obtained</option>
2582 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
2583 <option value="tissue_lib">tissue library from which sample was obtained</option>
2584 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
2585 <option value="base_count">number of base pairs</option>
2586 <option value="topology">sequence topology: circular or linear</option>
2587 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
2588 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
2589 <option value="first_public">date when made public</option>
2590 <option value="strain">strain from which sample was obtained</option>
2591 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
2592 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
2593 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
2594 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
2595 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
2596 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
2597 <option value="rna_class">classification of RNA</option>
2598 <option value="dataclass">sequence data class</option>
2599 <option value="gene">symbol of the gene corresponding to a sequence region</option>
2600 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
2601 </param>
2602 </when>
2603 <when value="fasta"/>
2604 </conditional>
2605 </when>
2606 <when value="assembly">
2607 <repeat name="queries" title="Add a query">
2608 <param name="combination_operation" type="select" label="Combination operation">
2609 <option value="AND">AND</option>
2610 <option value="OR">OR</option>
2611 <option value="NOT">NOT</option>
2612 </param>
2613 <conditional name="filter_field">
2614 <param name="field" type="select" label="Field to query">
2615 <option value="assembly_name">genome assembly name for all live versions</option>
2616 <option value="base_count">number of base pairs</option>
2617 <option value="strain">strain from which sample was obtained</option>
2618 <option value="study_description">detailed sequencing study description</option>
2619 <option value="accession">accession number</option>
2620 <option value="assembly_level">assembly level</option>
2621 <option value="sample_accession">sample accession number</option>
2622 <option value="assembly_title">brief genome assembly description</option>
2623 <option value="study_title">brief sequencing study description</option>
2624 <option value="genome_representation">whether this is a full or partial genome</option>
2625 <option value="study_name">sequencing study name</option>
2626 <option value="study_accession">study accession number</option>
2627 </param>
2628 <when value="assembly_name">
2629 <param name="operation" type="select" label="Operator">
2630 <option value="equal">equal</option>
2631 <option value="different">different</option>
2632 </param>
2633 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2634 </when>
2635 <when value="base_count">
2636 <param name="operation" type="select" label="Operator">
2637 <option value="equal">equal</option>
2638 <option value="different">different</option>
2639 <option value="lower">lower</option>
2640 <option value="equal or lower">equal or lower</option>
2641 <option value="higher">higher</option>
2642 <option value="equal or higher">equal or higher</option>
2643 </param>
2644 <param name="value" type="float" value="" label="Any integer"/>
2645 </when>
2646 <when value="strain">
2647 <param name="operation" type="select" label="Operator">
2648 <option value="equal">equal</option>
2649 <option value="different">different</option>
2650 </param>
2651 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2652 </when>
2653 <when value="study_description">
2654 <param name="operation" type="select" label="Operator">
2655 <option value="equal">equal</option>
2656 <option value="different">different</option>
2657 </param>
2658 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2659 </when>
2660 <when value="accession">
2661 <param name="operation" type="select" label="Operator">
2662 <option value="equal">equal</option>
2663 <option value="different">different</option>
2664 </param>
2665 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2666 </when>
2667 <when value="assembly_level">
2668 <param name="operation" type="select" label="Operator">
2669 <option value="equal">equal</option>
2670 <option value="different">different</option>
2671 </param>
2672 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2673 </when>
2674 <when value="sample_accession">
2675 <param name="operation" type="select" label="Operator">
2676 <option value="equal">equal</option>
2677 <option value="different">different</option>
2678 </param>
2679 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2680 </when>
2681 <when value="assembly_title">
2682 <param name="operation" type="select" label="Operator">
2683 <option value="equal">equal</option>
2684 <option value="different">different</option>
2685 </param>
2686 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2687 </when>
2688 <when value="study_title">
2689 <param name="operation" type="select" label="Operator">
2690 <option value="equal">equal</option>
2691 <option value="different">different</option>
2692 </param>
2693 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2694 </when>
2695 <when value="genome_representation">
2696 <param name="operation" type="select" label="Operator">
2697 <option value="equal">equal</option>
2698 <option value="different">different</option>
2699 </param>
2700 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2701 </when>
2702 <when value="study_name">
2703 <param name="operation" type="select" label="Operator">
2704 <option value="equal">equal</option>
2705 <option value="different">different</option>
2706 </param>
2707 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2708 </when>
2709 <when value="study_accession">
2710 <param name="operation" type="select" label="Operator">
2711 <option value="equal">equal</option>
2712 <option value="different">different</option>
2713 </param>
2714 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2715 </when>
2716 </conditional>
2717 </repeat>
2718 <conditional name="display_opt">
2719 <param argument="--display" type="select" label="Display option to specify the display format">
2720 <expand macro="display_options"/>
2721 </param>
2722 <when value="xml">
2723 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2724 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2725 </when>
2726 <when value="text">
2727 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2728 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2729 </when>
2730 <when value="fastq"/>
2731 <when value="html">
2732 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2733 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2734 </when>
2735 <when value="report">
2736 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
2737 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
2738 <param argument="--fields" type="select" multiple="true" label="Fields to return">
2739 <option value="accession">accession</option>
2740 <option value="study_accession">study_accession</option>
2741 <option value="sample_accession">sample_accession</option>
2742 <option value="assembly_name">assembly_name</option>
2743 <option value="assembly_title">assembly_title</option>
2744 <option value="study_name">study_name</option>
2745 <option value="study_title">study_title</option>
2746 <option value="study_description">study_description</option>
2747 <option value="tax_id">tax_id</option>
2748 <option value="scientific_name">scientific_name</option>
2749 <option value="strain">strain</option>
2750 <option value="base_count">base_count</option>
2751 <option value="assembly_level">assembly_level</option>
2752 <option value="genome_representation">genome_representation</option>
2753 </param>
2754 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
2755 <option value="assembly_name">genome assembly name for all live versions</option>
2756 <option value="base_count">number of base pairs</option>
2757 <option value="strain">strain from which sample was obtained</option>
2758 <option value="study_description">detailed sequencing study description</option>
2759 <option value="accession">accession number</option>
2760 <option value="assembly_level">assembly level</option>
2761 <option value="sample_accession">sample accession number</option>
2762 <option value="assembly_title">brief genome assembly description</option>
2763 <option value="study_title">brief sequencing study description</option>
2764 <option value="genome_representation">whether this is a full or partial genome</option>
2765 <option value="study_name">sequencing study name</option>
2766 <option value="study_accession">study accession number</option>
2767 </param>
2768 </when>
2769 <when value="fasta"/>
2770 </conditional>
2771 </when>
2772 <when value="sequence_release">
2773 <repeat name="queries" title="Add a query">
2774 <param name="combination_operation" type="select" label="Combination operation">
2775 <option value="AND">AND</option>
2776 <option value="OR">OR</option>
2777 <option value="NOT">NOT</option>
2778 </param>
2779 <conditional name="filter_field">
2780 <param name="field" type="select" label="Field to query">
2781 <option value="mol_type">in vivo molecule type of the sequence</option>
2782 <option value="last_updated">date when last updated</option>
2783 <option value="sequence_md5"></option>
2784 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
2785 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
2786 <option value="sex">sex of the organism from which the sample was obtained</option>
2787 <option value="keywords">keywords associated with sequence</option>
2788 <option value="collected_by">name of the person who collected the specimen</option>
2789 <option value="cell_line">cell line from which the sample was obtained</option>
2790 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
2791 <option value="bio_material">identifier for biological material including institute and collection code</option>
2792 <option value="identified_by">name of the taxonomist who identified the specimen</option>
2793 <option value="cell_type">cell type from which the sample was obtained</option>
2794 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
2795 <option value="tax_division">taxonomic division</option>
2796 <option value="collection_date">date that the specimen was collected</option>
2797 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
2798 <option value="altitude">Altitude (m)</option>
2799 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
2800 <option value="isolate">individual isolate from which sample was obtained</option>
2801 <option value="location">geographic location of isolation of the sample</option>
2802 <option value="study_accession">study accession number</option>
2803 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
2804 <option value="description">brief sequence description</option>
2805 <option value="accession">accession number</option>
2806 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
2807 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
2808 <option value="tissue_type">tissue type from which the sample was obtained</option>
2809 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
2810 <option value="tissue_lib">tissue library from which sample was obtained</option>
2811 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
2812 <option value="base_count">number of base pairs</option>
2813 <option value="topology">sequence topology: circular or linear</option>
2814 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
2815 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
2816 <option value="first_public">date when made public</option>
2817 <option value="strain">strain from which sample was obtained</option>
2818 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
2819 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
2820 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
2821 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
2822 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
2823 <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option>
2824 <option value="dataclass">sequence data class</option>
2825 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
2826 </param>
2827 <when value="mol_type">
2828 <param name="operation" type="select" label="Operator">
2829 <option value="equal">equal</option>
2830 <option value="different">different</option>
2831 </param>
2832 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2833 </when>
2834 <when value="last_updated">
2835 <param name="operation" type="select" label="Operator">
2836 <option value="equal">equal</option>
2837 <option value="different">different</option>
2838 <option value="lower">lower</option>
2839 <option value="equal or lower">equal or lower</option>
2840 <option value="higher">higher</option>
2841 <option value="equal or higher">equal or higher</option>
2842 </param>
2843 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
2844 </when>
2845 <when value="sequence_md5">
2846 <param name="operation" type="select" label="Operator">
2847 <option value="equal">equal</option>
2848 <option value="different">different</option>
2849 </param>
2850 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2851 </when>
2852 <when value="haplotype">
2853 <param name="operation" type="select" label="Operator">
2854 <option value="equal">equal</option>
2855 <option value="different">different</option>
2856 </param>
2857 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2858 </when>
2859 <when value="serotype">
2860 <param name="operation" type="select" label="Operator">
2861 <option value="equal">equal</option>
2862 <option value="different">different</option>
2863 </param>
2864 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2865 </when>
2866 <when value="sex">
2867 <param name="operation" type="select" label="Operator">
2868 <option value="equal">equal</option>
2869 <option value="different">different</option>
2870 </param>
2871 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2872 </when>
2873 <when value="keywords">
2874 <param name="operation" type="select" label="Operator">
2875 <option value="equal">equal</option>
2876 <option value="different">different</option>
2877 </param>
2878 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2879 </when>
2880 <when value="collected_by">
2881 <param name="operation" type="select" label="Operator">
2882 <option value="equal">equal</option>
2883 <option value="different">different</option>
2884 </param>
2885 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2886 </when>
2887 <when value="cell_line">
2888 <param name="operation" type="select" label="Operator">
2889 <option value="equal">equal</option>
2890 <option value="different">different</option>
2891 </param>
2892 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2893 </when>
2894 <when value="ecotype">
2895 <param name="operation" type="select" label="Operator">
2896 <option value="equal">equal</option>
2897 <option value="different">different</option>
2898 </param>
2899 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2900 </when>
2901 <when value="bio_material">
2902 <param name="operation" type="select" label="Operator">
2903 <option value="equal">equal</option>
2904 <option value="different">different</option>
2905 </param>
2906 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2907 </when>
2908 <when value="identified_by">
2909 <param name="operation" type="select" label="Operator">
2910 <option value="equal">equal</option>
2911 <option value="different">different</option>
2912 </param>
2913 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2914 </when>
2915 <when value="cell_type">
2916 <param name="operation" type="select" label="Operator">
2917 <option value="equal">equal</option>
2918 <option value="different">different</option>
2919 </param>
2920 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2921 </when>
2922 <when value="lab_host">
2923 <param name="operation" type="select" label="Operator">
2924 <option value="equal">equal</option>
2925 <option value="different">different</option>
2926 </param>
2927 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2928 </when>
2929 <when value="tax_division">
2930 <param name="operation" type="select" label="Operator">
2931 <option value="equal">equal</option>
2932 <option value="different">different</option>
2933 </param>
2934 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
2935 </when>
2936 <when value="collection_date">
2937 <param name="operation" type="select" label="Operator">
2938 <option value="equal">equal</option>
2939 <option value="different">different</option>
2940 <option value="lower">lower</option>
2941 <option value="equal or lower">equal or lower</option>
2942 <option value="higher">higher</option>
2943 <option value="equal or higher">equal or higher</option>
2944 </param>
2945 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
2946 </when>
2947 <when value="specimen_voucher">
2948 <param name="operation" type="select" label="Operator">
2949 <option value="equal">equal</option>
2950 <option value="different">different</option>
2951 </param>
2952 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2953 </when>
2954 <when value="altitude">
2955 <param name="operation" type="select" label="Operator">
2956 <option value="equal">equal</option>
2957 <option value="different">different</option>
2958 <option value="lower">lower</option>
2959 <option value="equal or lower">equal or lower</option>
2960 <option value="higher">higher</option>
2961 <option value="equal or higher">equal or higher</option>
2962 </param>
2963 <param name="value" type="float" value="" label="Any integer"/>
2964 </when>
2965 <when value="dev_stage">
2966 <param name="operation" type="select" label="Operator">
2967 <option value="equal">equal</option>
2968 <option value="different">different</option>
2969 </param>
2970 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2971 </when>
2972 <when value="isolate">
2973 <param name="operation" type="select" label="Operator">
2974 <option value="equal">equal</option>
2975 <option value="different">different</option>
2976 </param>
2977 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
2978 </when>
2979 <when value="location">
2980 <conditional name="op">
2981 <param name="operation" type="select" label="Operation">
2982 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
2983 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
2984 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
2985 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
2986 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
2987 <option value="geo_point">An exact lat/lon position</option>
2988 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
2989 </param>
2990 <when value="geo_box2">
2991 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
2992 </when>
2993 <when value="geo_box1">
2994 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
2995 </when>
2996 <when value="geo_circ">
2997 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
2998 </when>
2999 <when value="geo_lat">
3000 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
3001 </when>
3002 <when value="geo_south">
3003 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
3004 </when>
3005 <when value="geo_point">
3006 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
3007 </when>
3008 <when value="geo_north">
3009 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
3010 </when>
3011 </conditional>
3012 </when>
3013 <when value="study_accession">
3014 <param name="operation" type="select" label="Operator">
3015 <option value="equal">equal</option>
3016 <option value="different">different</option>
3017 </param>
3018 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3019 </when>
3020 <when value="germline">
3021 <param name="operation" type="select" label="Operator">
3022 <option value="equal">equal</option>
3023 </param>
3024 <param name="value" type="select" label="Value">
3025 <option value="yes">yes</option>
3026 <option value="true">true</option>
3027 <option value="no">no</option>
3028 <option value="false">false</option>
3029 </param>
3030 </when>
3031 <when value="description">
3032 <param name="operation" type="select" label="Operator">
3033 <option value="equal">equal</option>
3034 <option value="different">different</option>
3035 </param>
3036 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3037 </when>
3038 <when value="accession">
3039 <param name="operation" type="select" label="Operator">
3040 <option value="equal">equal</option>
3041 <option value="different">different</option>
3042 </param>
3043 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3044 </when>
3045 <when value="isolation_source">
3046 <param name="operation" type="select" label="Operator">
3047 <option value="equal">equal</option>
3048 <option value="different">different</option>
3049 </param>
3050 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3051 </when>
3052 <when value="mating_type">
3053 <param name="operation" type="select" label="Operator">
3054 <option value="equal">equal</option>
3055 <option value="different">different</option>
3056 </param>
3057 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3058 </when>
3059 <when value="tissue_type">
3060 <param name="operation" type="select" label="Operator">
3061 <option value="equal">equal</option>
3062 <option value="different">different</option>
3063 </param>
3064 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3065 </when>
3066 <when value="sub_strain">
3067 <param name="operation" type="select" label="Operator">
3068 <option value="equal">equal</option>
3069 <option value="different">different</option>
3070 </param>
3071 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3072 </when>
3073 <when value="tissue_lib">
3074 <param name="operation" type="select" label="Operator">
3075 <option value="equal">equal</option>
3076 <option value="different">different</option>
3077 </param>
3078 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3079 </when>
3080 <when value="cultivar">
3081 <param name="operation" type="select" label="Operator">
3082 <option value="equal">equal</option>
3083 <option value="different">different</option>
3084 </param>
3085 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3086 </when>
3087 <when value="base_count">
3088 <param name="operation" type="select" label="Operator">
3089 <option value="equal">equal</option>
3090 <option value="different">different</option>
3091 <option value="lower">lower</option>
3092 <option value="equal or lower">equal or lower</option>
3093 <option value="higher">higher</option>
3094 <option value="equal or higher">equal or higher</option>
3095 </param>
3096 <param name="value" type="float" value="" label="Any integer"/>
3097 </when>
3098 <when value="topology">
3099 <param name="operation" type="select" label="Operator">
3100 <option value="equal">equal</option>
3101 <option value="different">different</option>
3102 </param>
3103 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3104 </when>
3105 <when value="sub_species">
3106 <param name="operation" type="select" label="Operator">
3107 <option value="equal">equal</option>
3108 <option value="different">different</option>
3109 </param>
3110 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3111 </when>
3112 <when value="environmental_sample">
3113 <param name="operation" type="select" label="Operator">
3114 <option value="equal">equal</option>
3115 </param>
3116 <param name="value" type="select" label="Value">
3117 <option value="yes">yes</option>
3118 <option value="true">true</option>
3119 <option value="no">no</option>
3120 <option value="false">false</option>
3121 </param>
3122 </when>
3123 <when value="first_public">
3124 <param name="operation" type="select" label="Operator">
3125 <option value="equal">equal</option>
3126 <option value="different">different</option>
3127 <option value="lower">lower</option>
3128 <option value="equal or lower">equal or lower</option>
3129 <option value="higher">higher</option>
3130 <option value="equal or higher">equal or higher</option>
3131 </param>
3132 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
3133 </when>
3134 <when value="strain">
3135 <param name="operation" type="select" label="Operator">
3136 <option value="equal">equal</option>
3137 <option value="different">different</option>
3138 </param>
3139 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3140 </when>
3141 <when value="country">
3142 <param name="operation" type="select" label="Operator">
3143 <option value="equal">equal</option>
3144 <option value="different">different</option>
3145 </param>
3146 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3147 </when>
3148 <when value="variety">
3149 <param name="operation" type="select" label="Operator">
3150 <option value="equal">equal</option>
3151 <option value="different">different</option>
3152 </param>
3153 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3154 </when>
3155 <when value="host">
3156 <param name="operation" type="select" label="Operator">
3157 <option value="equal">equal</option>
3158 <option value="different">different</option>
3159 </param>
3160 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3161 </when>
3162 <when value="organelle">
3163 <param name="operation" type="select" label="Operator">
3164 <option value="equal">equal</option>
3165 <option value="different">different</option>
3166 </param>
3167 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3168 </when>
3169 <when value="serovar">
3170 <param name="operation" type="select" label="Operator">
3171 <option value="equal">equal</option>
3172 <option value="different">different</option>
3173 </param>
3174 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3175 </when>
3176 <when value="plasmid">
3177 <param name="operation" type="select" label="Operator">
3178 <option value="equal">equal</option>
3179 <option value="different">different</option>
3180 </param>
3181 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3182 </when>
3183 <when value="dataclass">
3184 <param name="operation" type="select" label="Operator">
3185 <option value="equal">equal</option>
3186 <option value="different">different</option>
3187 </param>
3188 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3189 </when>
3190 <when value="culture_collection">
3191 <param name="operation" type="select" label="Operator">
3192 <option value="equal">equal</option>
3193 <option value="different">different</option>
3194 </param>
3195 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3196 </when>
3197 </conditional>
3198 </repeat>
3199 <conditional name="display_opt">
3200 <param argument="--display" type="select" label="Display option to specify the display format">
3201 <expand macro="display_options"/>
3202 </param>
3203 <when value="xml">
3204 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3205 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3206 </when>
3207 <when value="text">
3208 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3209 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3210 </when>
3211 <when value="fastq"/>
3212 <when value="html">
3213 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3214 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3215 </when>
3216 <when value="report">
3217 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3218 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3219 <param argument="--fields" type="select" multiple="true" label="Fields to return">
3220 <option value="accession">accession</option>
3221 <option value="base_count">base_count</option>
3222 <option value="bio_material">bio_material</option>
3223 <option value="cell_line">cell_line</option>
3224 <option value="cell_type">cell_type</option>
3225 <option value="collected_by">collected_by</option>
3226 <option value="collection_date">collection_date</option>
3227 <option value="country">country</option>
3228 <option value="cultivar">cultivar</option>
3229 <option value="culture_collection">culture_collection</option>
3230 <option value="dataclass">dataclass</option>
3231 <option value="description">description</option>
3232 <option value="dev_stage">dev_stage</option>
3233 <option value="ecotype">ecotype</option>
3234 <option value="environmental_sample">environmental_sample</option>
3235 <option value="first_public">first_public</option>
3236 <option value="germline">germline</option>
3237 <option value="host">host</option>
3238 <option value="identified_by">identified_by</option>
3239 <option value="isolate">isolate</option>
3240 <option value="isolation_source">isolation_source</option>
3241 <option value="keywords">keywords</option>
3242 <option value="lab_host">lab_host</option>
3243 <option value="last_updated">last_updated</option>
3244 <option value="location">location</option>
3245 <option value="mating_type">mating_type</option>
3246 <option value="mol_type">mol_type</option>
3247 <option value="organelle">organelle</option>
3248 <option value="serotype">serotype</option>
3249 <option value="serovar">serovar</option>
3250 <option value="sex">sex</option>
3251 <option value="submitted_sex">submitted_sex</option>
3252 <option value="specimen_voucher">specimen_voucher</option>
3253 <option value="strain">strain</option>
3254 <option value="sub_species">sub_species</option>
3255 <option value="sub_strain">sub_strain</option>
3256 <option value="tax_division">tax_division</option>
3257 <option value="tissue_lib">tissue_lib</option>
3258 <option value="tissue_type">tissue_type</option>
3259 <option value="topology">topology</option>
3260 <option value="variety">variety</option>
3261 <option value="tax_id">tax_id</option>
3262 <option value="scientific_name">scientific_name</option>
3263 <option value="altitude">altitude</option>
3264 <option value="haplotype">haplotype</option>
3265 <option value="plasmid">plasmid</option>
3266 <option value="study_accession">study_accession</option>
3267 <option value="sequence_md5">sequence_md5</option>
3268 </param>
3269 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
3270 <option value="mol_type">in vivo molecule type of the sequence</option>
3271 <option value="last_updated">date when last updated</option>
3272 <option value="sequence_md5"></option>
3273 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
3274 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
3275 <option value="sex">sex of the organism from which the sample was obtained</option>
3276 <option value="keywords">keywords associated with sequence</option>
3277 <option value="collected_by">name of the person who collected the specimen</option>
3278 <option value="cell_line">cell line from which the sample was obtained</option>
3279 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
3280 <option value="bio_material">identifier for biological material including institute and collection code</option>
3281 <option value="identified_by">name of the taxonomist who identified the specimen</option>
3282 <option value="cell_type">cell type from which the sample was obtained</option>
3283 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
3284 <option value="tax_division">taxonomic division</option>
3285 <option value="collection_date">date that the specimen was collected</option>
3286 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
3287 <option value="altitude">Altitude (m)</option>
3288 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
3289 <option value="isolate">individual isolate from which sample was obtained</option>
3290 <option value="location">geographic location of isolation of the sample</option>
3291 <option value="study_accession">study accession number</option>
3292 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
3293 <option value="description">brief sequence description</option>
3294 <option value="accession">accession number</option>
3295 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
3296 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
3297 <option value="tissue_type">tissue type from which the sample was obtained</option>
3298 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
3299 <option value="tissue_lib">tissue library from which sample was obtained</option>
3300 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
3301 <option value="base_count">number of base pairs</option>
3302 <option value="topology">sequence topology: circular or linear</option>
3303 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
3304 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
3305 <option value="first_public">date when made public</option>
3306 <option value="strain">strain from which sample was obtained</option>
3307 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
3308 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
3309 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
3310 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
3311 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
3312 <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option>
3313 <option value="dataclass">sequence data class</option>
3314 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
3315 </param>
3316 </when>
3317 <when value="fasta"/>
3318 </conditional>
3319 </when>
3320 <when value="wgs_set">
3321 <repeat name="queries" title="Add a query">
3322 <param name="combination_operation" type="select" label="Combination operation">
3323 <option value="AND">AND</option>
3324 <option value="OR">OR</option>
3325 <option value="NOT">NOT</option>
3326 </param>
3327 <conditional name="filter_field">
3328 <param name="field" type="select" label="Field to query">
3329 <option value="mol_type">in vivo molecule type of the sequence</option>
3330 <option value="last_updated">date when last updated</option>
3331 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
3332 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
3333 <option value="accession">accession number</option>
3334 <option value="sex">sex of the organism from which the sample was obtained</option>
3335 <option value="cell_line">cell line from which the sample was obtained</option>
3336 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
3337 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
3338 <option value="bio_material">identifier for biological material including institute and collection code</option>
3339 <option value="identified_by">name of the taxonomist who identified the specimen</option>
3340 <option value="cell_type">cell type from which the sample was obtained</option>
3341 <option value="tax_division">taxonomic division</option>
3342 <option value="collection_date">date that the specimen was collected</option>
3343 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
3344 <option value="altitude">Altitude (m)</option>
3345 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
3346 <option value="isolate">individual isolate from which sample was obtained</option>
3347 <option value="location">geographic location of isolation of the sample</option>
3348 <option value="study_accession">study accession number</option>
3349 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
3350 <option value="description">brief sequence description</option>
3351 <option value="tissue_lib">tissue library from which sample was obtained</option>
3352 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
3353 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
3354 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
3355 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
3356 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
3357 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
3358 <option value="collected_by">name of the person who collected the specimen</option>
3359 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
3360 <option value="first_public">date when made public</option>
3361 <option value="strain">strain from which sample was obtained</option>
3362 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
3363 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
3364 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
3365 <option value="tissue_type">tissue type from which the sample was obtained</option>
3366 <option value="keywords">keywords associated with sequence</option>
3367 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
3368 </param>
3369 <when value="mol_type">
3370 <param name="operation" type="select" label="Operator">
3371 <option value="equal">equal</option>
3372 <option value="different">different</option>
3373 </param>
3374 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3375 </when>
3376 <when value="last_updated">
3377 <param name="operation" type="select" label="Operator">
3378 <option value="equal">equal</option>
3379 <option value="different">different</option>
3380 <option value="lower">lower</option>
3381 <option value="equal or lower">equal or lower</option>
3382 <option value="higher">higher</option>
3383 <option value="equal or higher">equal or higher</option>
3384 </param>
3385 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
3386 </when>
3387 <when value="lab_host">
3388 <param name="operation" type="select" label="Operator">
3389 <option value="equal">equal</option>
3390 <option value="different">different</option>
3391 </param>
3392 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3393 </when>
3394 <when value="haplotype">
3395 <param name="operation" type="select" label="Operator">
3396 <option value="equal">equal</option>
3397 <option value="different">different</option>
3398 </param>
3399 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3400 </when>
3401 <when value="accession">
3402 <param name="operation" type="select" label="Operator">
3403 <option value="equal">equal</option>
3404 <option value="different">different</option>
3405 </param>
3406 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3407 </when>
3408 <when value="sex">
3409 <param name="operation" type="select" label="Operator">
3410 <option value="equal">equal</option>
3411 <option value="different">different</option>
3412 </param>
3413 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3414 </when>
3415 <when value="cell_line">
3416 <param name="operation" type="select" label="Operator">
3417 <option value="equal">equal</option>
3418 <option value="different">different</option>
3419 </param>
3420 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3421 </when>
3422 <when value="host">
3423 <param name="operation" type="select" label="Operator">
3424 <option value="equal">equal</option>
3425 <option value="different">different</option>
3426 </param>
3427 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3428 </when>
3429 <when value="ecotype">
3430 <param name="operation" type="select" label="Operator">
3431 <option value="equal">equal</option>
3432 <option value="different">different</option>
3433 </param>
3434 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3435 </when>
3436 <when value="bio_material">
3437 <param name="operation" type="select" label="Operator">
3438 <option value="equal">equal</option>
3439 <option value="different">different</option>
3440 </param>
3441 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3442 </when>
3443 <when value="identified_by">
3444 <param name="operation" type="select" label="Operator">
3445 <option value="equal">equal</option>
3446 <option value="different">different</option>
3447 </param>
3448 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3449 </when>
3450 <when value="cell_type">
3451 <param name="operation" type="select" label="Operator">
3452 <option value="equal">equal</option>
3453 <option value="different">different</option>
3454 </param>
3455 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3456 </when>
3457 <when value="tax_division">
3458 <param name="operation" type="select" label="Operator">
3459 <option value="equal">equal</option>
3460 <option value="different">different</option>
3461 </param>
3462 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3463 </when>
3464 <when value="collection_date">
3465 <param name="operation" type="select" label="Operator">
3466 <option value="equal">equal</option>
3467 <option value="different">different</option>
3468 <option value="lower">lower</option>
3469 <option value="equal or lower">equal or lower</option>
3470 <option value="higher">higher</option>
3471 <option value="equal or higher">equal or higher</option>
3472 </param>
3473 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
3474 </when>
3475 <when value="specimen_voucher">
3476 <param name="operation" type="select" label="Operator">
3477 <option value="equal">equal</option>
3478 <option value="different">different</option>
3479 </param>
3480 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3481 </when>
3482 <when value="altitude">
3483 <param name="operation" type="select" label="Operator">
3484 <option value="equal">equal</option>
3485 <option value="different">different</option>
3486 <option value="lower">lower</option>
3487 <option value="equal or lower">equal or lower</option>
3488 <option value="higher">higher</option>
3489 <option value="equal or higher">equal or higher</option>
3490 </param>
3491 <param name="value" type="float" value="" label="Any integer"/>
3492 </when>
3493 <when value="dev_stage">
3494 <param name="operation" type="select" label="Operator">
3495 <option value="equal">equal</option>
3496 <option value="different">different</option>
3497 </param>
3498 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3499 </when>
3500 <when value="isolate">
3501 <param name="operation" type="select" label="Operator">
3502 <option value="equal">equal</option>
3503 <option value="different">different</option>
3504 </param>
3505 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3506 </when>
3507 <when value="location">
3508 <conditional name="op">
3509 <param name="operation" type="select" label="Operation">
3510 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
3511 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
3512 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
3513 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
3514 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
3515 <option value="geo_point">An exact lat/lon position</option>
3516 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
3517 </param>
3518 <when value="geo_box2">
3519 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
3520 </when>
3521 <when value="geo_box1">
3522 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
3523 </when>
3524 <when value="geo_circ">
3525 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
3526 </when>
3527 <when value="geo_lat">
3528 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
3529 </when>
3530 <when value="geo_south">
3531 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
3532 </when>
3533 <when value="geo_point">
3534 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
3535 </when>
3536 <when value="geo_north">
3537 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
3538 </when>
3539 </conditional>
3540 </when>
3541 <when value="study_accession">
3542 <param name="operation" type="select" label="Operator">
3543 <option value="equal">equal</option>
3544 <option value="different">different</option>
3545 </param>
3546 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3547 </when>
3548 <when value="germline">
3549 <param name="operation" type="select" label="Operator">
3550 <option value="equal">equal</option>
3551 </param>
3552 <param name="value" type="select" label="Value">
3553 <option value="yes">yes</option>
3554 <option value="true">true</option>
3555 <option value="no">no</option>
3556 <option value="false">false</option>
3557 </param>
3558 </when>
3559 <when value="description">
3560 <param name="operation" type="select" label="Operator">
3561 <option value="equal">equal</option>
3562 <option value="different">different</option>
3563 </param>
3564 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3565 </when>
3566 <when value="tissue_lib">
3567 <param name="operation" type="select" label="Operator">
3568 <option value="equal">equal</option>
3569 <option value="different">different</option>
3570 </param>
3571 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3572 </when>
3573 <when value="isolation_source">
3574 <param name="operation" type="select" label="Operator">
3575 <option value="equal">equal</option>
3576 <option value="different">different</option>
3577 </param>
3578 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3579 </when>
3580 <when value="mating_type">
3581 <param name="operation" type="select" label="Operator">
3582 <option value="equal">equal</option>
3583 <option value="different">different</option>
3584 </param>
3585 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3586 </when>
3587 <when value="serovar">
3588 <param name="operation" type="select" label="Operator">
3589 <option value="equal">equal</option>
3590 <option value="different">different</option>
3591 </param>
3592 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3593 </when>
3594 <when value="serotype">
3595 <param name="operation" type="select" label="Operator">
3596 <option value="equal">equal</option>
3597 <option value="different">different</option>
3598 </param>
3599 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3600 </when>
3601 <when value="sub_strain">
3602 <param name="operation" type="select" label="Operator">
3603 <option value="equal">equal</option>
3604 <option value="different">different</option>
3605 </param>
3606 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3607 </when>
3608 <when value="cultivar">
3609 <param name="operation" type="select" label="Operator">
3610 <option value="equal">equal</option>
3611 <option value="different">different</option>
3612 </param>
3613 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3614 </when>
3615 <when value="collected_by">
3616 <param name="operation" type="select" label="Operator">
3617 <option value="equal">equal</option>
3618 <option value="different">different</option>
3619 </param>
3620 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3621 </when>
3622 <when value="sub_species">
3623 <param name="operation" type="select" label="Operator">
3624 <option value="equal">equal</option>
3625 <option value="different">different</option>
3626 </param>
3627 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3628 </when>
3629 <when value="first_public">
3630 <param name="operation" type="select" label="Operator">
3631 <option value="equal">equal</option>
3632 <option value="different">different</option>
3633 <option value="lower">lower</option>
3634 <option value="equal or lower">equal or lower</option>
3635 <option value="higher">higher</option>
3636 <option value="equal or higher">equal or higher</option>
3637 </param>
3638 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
3639 </when>
3640 <when value="strain">
3641 <param name="operation" type="select" label="Operator">
3642 <option value="equal">equal</option>
3643 <option value="different">different</option>
3644 </param>
3645 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3646 </when>
3647 <when value="country">
3648 <param name="operation" type="select" label="Operator">
3649 <option value="equal">equal</option>
3650 <option value="different">different</option>
3651 </param>
3652 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3653 </when>
3654 <when value="variety">
3655 <param name="operation" type="select" label="Operator">
3656 <option value="equal">equal</option>
3657 <option value="different">different</option>
3658 </param>
3659 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3660 </when>
3661 <when value="environmental_sample">
3662 <param name="operation" type="select" label="Operator">
3663 <option value="equal">equal</option>
3664 </param>
3665 <param name="value" type="select" label="Value">
3666 <option value="yes">yes</option>
3667 <option value="true">true</option>
3668 <option value="no">no</option>
3669 <option value="false">false</option>
3670 </param>
3671 </when>
3672 <when value="tissue_type">
3673 <param name="operation" type="select" label="Operator">
3674 <option value="equal">equal</option>
3675 <option value="different">different</option>
3676 </param>
3677 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3678 </when>
3679 <when value="keywords">
3680 <param name="operation" type="select" label="Operator">
3681 <option value="equal">equal</option>
3682 <option value="different">different</option>
3683 </param>
3684 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3685 </when>
3686 <when value="culture_collection">
3687 <param name="operation" type="select" label="Operator">
3688 <option value="equal">equal</option>
3689 <option value="different">different</option>
3690 </param>
3691 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3692 </when>
3693 </conditional>
3694 </repeat>
3695 <conditional name="display_opt">
3696 <param argument="--display" type="select" label="Display option to specify the display format">
3697 <expand macro="display_options"/>
3698 </param>
3699 <when value="xml">
3700 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3701 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3702 </when>
3703 <when value="text">
3704 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3705 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3706 </when>
3707 <when value="fastq"/>
3708 <when value="html">
3709 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3710 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3711 </when>
3712 <when value="report">
3713 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3714 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3715 <param argument="--fields" type="select" multiple="true" label="Fields to return">
3716 <option value="accession">accession</option>
3717 <option value="bio_material">bio_material</option>
3718 <option value="cell_line">cell_line</option>
3719 <option value="cell_type">cell_type</option>
3720 <option value="collected_by">collected_by</option>
3721 <option value="collection_date">collection_date</option>
3722 <option value="country">country</option>
3723 <option value="cultivar">cultivar</option>
3724 <option value="culture_collection">culture_collection</option>
3725 <option value="description">description</option>
3726 <option value="dev_stage">dev_stage</option>
3727 <option value="ecotype">ecotype</option>
3728 <option value="environmental_sample">environmental_sample</option>
3729 <option value="first_public">first_public</option>
3730 <option value="germline">germline</option>
3731 <option value="host">host</option>
3732 <option value="identified_by">identified_by</option>
3733 <option value="isolate">isolate</option>
3734 <option value="isolation_source">isolation_source</option>
3735 <option value="keywords">keywords</option>
3736 <option value="lab_host">lab_host</option>
3737 <option value="last_updated">last_updated</option>
3738 <option value="location">location</option>
3739 <option value="mating_type">mating_type</option>
3740 <option value="mol_type">mol_type</option>
3741 <option value="serotype">serotype</option>
3742 <option value="serovar">serovar</option>
3743 <option value="sex">sex</option>
3744 <option value="submitted_sex">submitted_sex</option>
3745 <option value="specimen_voucher">specimen_voucher</option>
3746 <option value="strain">strain</option>
3747 <option value="sub_species">sub_species</option>
3748 <option value="sub_strain">sub_strain</option>
3749 <option value="tax_division">tax_division</option>
3750 <option value="tissue_lib">tissue_lib</option>
3751 <option value="tissue_type">tissue_type</option>
3752 <option value="variety">variety</option>
3753 <option value="tax_id">tax_id</option>
3754 <option value="scientific_name">scientific_name</option>
3755 <option value="altitude">altitude</option>
3756 <option value="haplotype">haplotype</option>
3757 <option value="study_accession">study_accession</option>
3758 <option value="set_files">set_files</option>
3759 </param>
3760 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
3761 <option value="mol_type">in vivo molecule type of the sequence</option>
3762 <option value="last_updated">date when last updated</option>
3763 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
3764 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
3765 <option value="accession">accession number</option>
3766 <option value="sex">sex of the organism from which the sample was obtained</option>
3767 <option value="cell_line">cell line from which the sample was obtained</option>
3768 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
3769 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
3770 <option value="bio_material">identifier for biological material including institute and collection code</option>
3771 <option value="identified_by">name of the taxonomist who identified the specimen</option>
3772 <option value="cell_type">cell type from which the sample was obtained</option>
3773 <option value="tax_division">taxonomic division</option>
3774 <option value="collection_date">date that the specimen was collected</option>
3775 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
3776 <option value="altitude">Altitude (m)</option>
3777 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
3778 <option value="isolate">individual isolate from which sample was obtained</option>
3779 <option value="location">geographic location of isolation of the sample</option>
3780 <option value="study_accession">study accession number</option>
3781 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
3782 <option value="description">brief sequence description</option>
3783 <option value="tissue_lib">tissue library from which sample was obtained</option>
3784 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
3785 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
3786 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
3787 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
3788 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
3789 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
3790 <option value="collected_by">name of the person who collected the specimen</option>
3791 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
3792 <option value="first_public">date when made public</option>
3793 <option value="strain">strain from which sample was obtained</option>
3794 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
3795 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
3796 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
3797 <option value="tissue_type">tissue type from which the sample was obtained</option>
3798 <option value="keywords">keywords associated with sequence</option>
3799 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
3800 </param>
3801 </when>
3802 <when value="fasta"/>
3803 </conditional>
3804 </when>
3805 <when value="study">
3806 <repeat name="queries" title="Add a query">
3807 <param name="combination_operation" type="select" label="Combination operation">
3808 <option value="AND">AND</option>
3809 <option value="OR">OR</option>
3810 <option value="NOT">NOT</option>
3811 </param>
3812 <conditional name="filter_field">
3813 <param name="field" type="select" label="Field to query">
3814 <option value="broker_name">broker name</option>
3815 <option value="last_updated">date when last updated</option>
3816 <option value="center_name">Submitting center</option>
3817 <option value="study_description">detailed sequencing study description</option>
3818 <option value="breed">breed</option>
3819 <option value="isolate">individual isolate from which sample was obtained</option>
3820 <option value="study_name">sequencing study name</option>
3821 <option value="geo_accession">GEO accession</option>
3822 <option value="strain">strain from which sample was obtained</option>
3823 <option value="secondary_study_accession">project accession number</option>
3824 <option value="keywords">keywords associated with sequence</option>
3825 <option value="study_title">brief sequencing study description</option>
3826 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
3827 <option value="study_accession">study accession number</option>
3828 </param>
3829 <when value="broker_name">
3830 <param name="operation" type="select" label="Operator">
3831 <option value="equal">equal</option>
3832 <option value="different">different</option>
3833 </param>
3834 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
3835 </when>
3836 <when value="last_updated">
3837 <param name="operation" type="select" label="Operator">
3838 <option value="equal">equal</option>
3839 <option value="different">different</option>
3840 <option value="lower">lower</option>
3841 <option value="equal or lower">equal or lower</option>
3842 <option value="higher">higher</option>
3843 <option value="equal or higher">equal or higher</option>
3844 </param>
3845 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
3846 </when>
3847 <when value="center_name">
3848 <param name="operation" type="select" label="Operator">
3849 <option value="equal">equal</option>
3850 <option value="different">different</option>
3851 </param>
3852 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3853 </when>
3854 <when value="study_description">
3855 <param name="operation" type="select" label="Operator">
3856 <option value="equal">equal</option>
3857 <option value="different">different</option>
3858 </param>
3859 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3860 </when>
3861 <when value="breed">
3862 <param name="operation" type="select" label="Operator">
3863 <option value="equal">equal</option>
3864 <option value="different">different</option>
3865 </param>
3866 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3867 </when>
3868 <when value="isolate">
3869 <param name="operation" type="select" label="Operator">
3870 <option value="equal">equal</option>
3871 <option value="different">different</option>
3872 </param>
3873 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3874 </when>
3875 <when value="study_name">
3876 <param name="operation" type="select" label="Operator">
3877 <option value="equal">equal</option>
3878 <option value="different">different</option>
3879 </param>
3880 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3881 </when>
3882 <when value="geo_accession">
3883 <param name="operation" type="select" label="Operator">
3884 <option value="equal">equal</option>
3885 <option value="different">different</option>
3886 </param>
3887 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3888 </when>
3889 <when value="strain">
3890 <param name="operation" type="select" label="Operator">
3891 <option value="equal">equal</option>
3892 <option value="different">different</option>
3893 </param>
3894 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3895 </when>
3896 <when value="secondary_study_accession">
3897 <param name="operation" type="select" label="Operator">
3898 <option value="equal">equal</option>
3899 <option value="different">different</option>
3900 </param>
3901 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3902 </when>
3903 <when value="keywords">
3904 <param name="operation" type="select" label="Operator">
3905 <option value="equal">equal</option>
3906 <option value="different">different</option>
3907 </param>
3908 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3909 </when>
3910 <when value="study_title">
3911 <param name="operation" type="select" label="Operator">
3912 <option value="equal">equal</option>
3913 <option value="different">different</option>
3914 </param>
3915 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3916 </when>
3917 <when value="cultivar">
3918 <param name="operation" type="select" label="Operator">
3919 <option value="equal">equal</option>
3920 <option value="different">different</option>
3921 </param>
3922 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3923 </when>
3924 <when value="study_accession">
3925 <param name="operation" type="select" label="Operator">
3926 <option value="equal">equal</option>
3927 <option value="different">different</option>
3928 </param>
3929 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
3930 </when>
3931 </conditional>
3932 </repeat>
3933 <conditional name="display_opt">
3934 <param argument="--display" type="select" label="Display option to specify the display format">
3935 <expand macro="display_options"/>
3936 </param>
3937 <when value="xml">
3938 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3939 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3940 </when>
3941 <when value="text">
3942 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3943 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3944 </when>
3945 <when value="fastq"/>
3946 <when value="html">
3947 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3948 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3949 </when>
3950 <when value="report">
3951 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
3952 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
3953 <param argument="--fields" type="select" multiple="true" label="Fields to return">
3954 <option value="study_accession">study_accession</option>
3955 <option value="secondary_study_accession">secondary_study_accession</option>
3956 <option value="study_description">study_description</option>
3957 <option value="study_name">study_name</option>
3958 <option value="study_title">study_title</option>
3959 <option value="tax_id">tax_id</option>
3960 <option value="scientific_name">scientific_name</option>
3961 <option value="strain">strain</option>
3962 <option value="breed">breed</option>
3963 <option value="cultivar">cultivar</option>
3964 <option value="isolate">isolate</option>
3965 <option value="center_name">center_name</option>
3966 <option value="broker_name">broker_name</option>
3967 <option value="keywords">keywords</option>
3968 <option value="geo_accession">geo_accession</option>
3969 <option value="last_updated">last_updated</option>
3970 </param>
3971 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
3972 <option value="broker_name">broker name</option>
3973 <option value="last_updated">date when last updated</option>
3974 <option value="center_name">Submitting center</option>
3975 <option value="study_description">detailed sequencing study description</option>
3976 <option value="breed">breed</option>
3977 <option value="isolate">individual isolate from which sample was obtained</option>
3978 <option value="study_name">sequencing study name</option>
3979 <option value="geo_accession">GEO accession</option>
3980 <option value="strain">strain from which sample was obtained</option>
3981 <option value="secondary_study_accession">project accession number</option>
3982 <option value="keywords">keywords associated with sequence</option>
3983 <option value="study_title">brief sequencing study description</option>
3984 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
3985 <option value="study_accession">study accession number</option>
3986 </param>
3987 </when>
3988 <when value="fasta"/>
3989 </conditional>
3990 </when>
3991 <when value="taxon">
3992 <repeat name="queries" title="Add a query">
3993 <param name="combination_operation" type="select" label="Combination operation">
3994 <option value="AND">AND</option>
3995 <option value="OR">OR</option>
3996 <option value="NOT">NOT</option>
3997 </param>
3998 <conditional name="filter_field">
3999 <param name="field" type="select" label="Field to query">
4000 </param>
4001 </conditional>
4002 </repeat>
4003 <conditional name="display_opt">
4004 <param argument="--display" type="select" label="Display option to specify the display format">
4005 <expand macro="display_options"/>
4006 </param>
4007 <when value="xml">
4008 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4009 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4010 </when>
4011 <when value="text">
4012 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4013 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4014 </when>
4015 <when value="fastq"/>
4016 <when value="html">
4017 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4018 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4019 </when>
4020 <when value="report">
4021 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4022 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4023 <param argument="--fields" type="select" multiple="true" label="Fields to return">
4024 <option value="tax_id">tax_id</option>
4025 <option value="taxon_title">taxon_title</option>
4026 <option value="scientific_name">scientific_name</option>
4027 </param>
4028 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
4029 </param>
4030 </when>
4031 <when value="fasta"/>
4032 </conditional>
4033 </when>
4034 <when value="coding_release">
4035 <repeat name="queries" title="Add a query">
4036 <param name="combination_operation" type="select" label="Combination operation">
4037 <option value="AND">AND</option>
4038 <option value="OR">OR</option>
4039 <option value="NOT">NOT</option>
4040 </param>
4041 <conditional name="filter_field">
4042 <param name="field" type="select" label="Field to query">
4043 <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option>
4044 <option value="mol_type">in vivo molecule type of the sequence</option>
4045 <option value="last_updated">date when last updated</option>
4046 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
4047 <option value="transl_except">a single codon translation that does not conform to genetic code</option>
4048 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
4049 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
4050 <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option>
4051 <option value="sex">sex of the organism from which the sample was obtained</option>
4052 <option value="pseudo_gene">indicates that this feature is a pseudogene</option>
4053 <option value="standard_name">accepted standard name for a feature</option>
4054 <option value="collected_by">name of the person who collected the specimen</option>
4055 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
4056 <option value="cell_type">cell type from which the sample was obtained</option>
4057 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
4058 <option value="inference">a structured description of non-experimental evidence</option>
4059 <option value="bio_material">identifier for biological material including institute and collection code</option>
4060 <option value="parent_accession">parent sequence accession number</option>
4061 <option value="identified_by">name of the taxonomist who identified the specimen</option>
4062 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
4063 <option value="sequence_md5"></option>
4064 <option value="tax_division">taxonomic division</option>
4065 <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
4066 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
4067 <option value="altitude">Altitude (m)</option>
4068 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
4069 <option value="isolate">individual isolate from which sample was obtained</option>
4070 <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option>
4071 <option value="note">any comment or additional information</option>
4072 <option value="experiment">a brief description of the nature of the experimental evidence</option>
4073 <option value="location">geographic location of isolation of the sample</option>
4074 <option value="collection_date">date that the specimen was collected</option>
4075 <option value="allele">name of the allele for the given gene</option>
4076 <option value="protein_id">a stable protein identifier issued by INSDC</option>
4077 <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option>
4078 <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option>
4079 <option value="function">function attributed to a sequence</option>
4080 <option value="map">genomic map position of feature</option>
4081 <option value="product">name of the product associated with the feature</option>
4082 <option value="description">brief sequence description</option>
4083 <option value="cell_line">cell line from which the sample was obtained</option>
4084 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
4085 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
4086 <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option>
4087 <option value="accession">accession number</option>
4088 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
4089 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
4090 <option value="tissue_type">tissue type from which the sample was obtained</option>
4091 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
4092 <option value="tissue_lib">tissue library from which sample was obtained</option>
4093 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
4094 <option value="base_count">number of base pairs</option>
4095 <option value="topology">sequence topology: circular or linear</option>
4096 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
4097 <option value="first_public">date when made public</option>
4098 <option value="strain">strain from which sample was obtained</option>
4099 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
4100 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
4101 <option value="pseudo">the feature is non-functional</option>
4102 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
4103 <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option>
4104 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
4105 <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option>
4106 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
4107 <option value="keywords">keywords associated with sequence</option>
4108 <option value="dataclass">sequence data class</option>
4109 <option value="gene">symbol of the gene corresponding to a sequence region</option>
4110 <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option>
4111 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
4112 </param>
4113 <when value="operon">
4114 <param name="operation" type="select" label="Operator">
4115 <option value="equal">equal</option>
4116 <option value="different">different</option>
4117 </param>
4118 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4119 </when>
4120 <when value="mol_type">
4121 <param name="operation" type="select" label="Operator">
4122 <option value="equal">equal</option>
4123 <option value="different">different</option>
4124 </param>
4125 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4126 </when>
4127 <when value="last_updated">
4128 <param name="operation" type="select" label="Operator">
4129 <option value="equal">equal</option>
4130 <option value="different">different</option>
4131 <option value="lower">lower</option>
4132 <option value="equal or lower">equal or lower</option>
4133 <option value="higher">higher</option>
4134 <option value="equal or higher">equal or higher</option>
4135 </param>
4136 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
4137 </when>
4138 <when value="lab_host">
4139 <param name="operation" type="select" label="Operator">
4140 <option value="equal">equal</option>
4141 <option value="different">different</option>
4142 </param>
4143 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4144 </when>
4145 <when value="transl_except">
4146 <param name="operation" type="select" label="Operator">
4147 <option value="equal">equal</option>
4148 <option value="different">different</option>
4149 </param>
4150 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4151 </when>
4152 <when value="haplotype">
4153 <param name="operation" type="select" label="Operator">
4154 <option value="equal">equal</option>
4155 <option value="different">different</option>
4156 </param>
4157 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4158 </when>
4159 <when value="serotype">
4160 <param name="operation" type="select" label="Operator">
4161 <option value="equal">equal</option>
4162 <option value="different">different</option>
4163 </param>
4164 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4165 </when>
4166 <when value="trans_splicing">
4167 <param name="operation" type="select" label="Operator">
4168 <option value="equal">equal</option>
4169 </param>
4170 <param name="value" type="select" label="Value">
4171 <option value="yes">yes</option>
4172 <option value="true">true</option>
4173 <option value="no">no</option>
4174 <option value="false">false</option>
4175 </param>
4176 </when>
4177 <when value="sex">
4178 <param name="operation" type="select" label="Operator">
4179 <option value="equal">equal</option>
4180 <option value="different">different</option>
4181 </param>
4182 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4183 </when>
4184 <when value="pseudo_gene">
4185 <param name="operation" type="select" label="Operator">
4186 <option value="equal">equal</option>
4187 <option value="different">different</option>
4188 </param>
4189 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4190 </when>
4191 <when value="standard_name">
4192 <param name="operation" type="select" label="Operator">
4193 <option value="equal">equal</option>
4194 <option value="different">different</option>
4195 </param>
4196 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4197 </when>
4198 <when value="collected_by">
4199 <param name="operation" type="select" label="Operator">
4200 <option value="equal">equal</option>
4201 <option value="different">different</option>
4202 </param>
4203 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4204 </when>
4205 <when value="germline">
4206 <param name="operation" type="select" label="Operator">
4207 <option value="equal">equal</option>
4208 </param>
4209 <param name="value" type="select" label="Value">
4210 <option value="yes">yes</option>
4211 <option value="true">true</option>
4212 <option value="no">no</option>
4213 <option value="false">false</option>
4214 </param>
4215 </when>
4216 <when value="cell_type">
4217 <param name="operation" type="select" label="Operator">
4218 <option value="equal">equal</option>
4219 <option value="different">different</option>
4220 </param>
4221 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4222 </when>
4223 <when value="host">
4224 <param name="operation" type="select" label="Operator">
4225 <option value="equal">equal</option>
4226 <option value="different">different</option>
4227 </param>
4228 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4229 </when>
4230 <when value="inference">
4231 <param name="operation" type="select" label="Operator">
4232 <option value="equal">equal</option>
4233 <option value="different">different</option>
4234 </param>
4235 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4236 </when>
4237 <when value="bio_material">
4238 <param name="operation" type="select" label="Operator">
4239 <option value="equal">equal</option>
4240 <option value="different">different</option>
4241 </param>
4242 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4243 </when>
4244 <when value="parent_accession">
4245 <param name="operation" type="select" label="Operator">
4246 <option value="equal">equal</option>
4247 <option value="different">different</option>
4248 </param>
4249 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4250 </when>
4251 <when value="identified_by">
4252 <param name="operation" type="select" label="Operator">
4253 <option value="equal">equal</option>
4254 <option value="different">different</option>
4255 </param>
4256 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4257 </when>
4258 <when value="locus_tag">
4259 <param name="operation" type="select" label="Operator">
4260 <option value="equal">equal</option>
4261 <option value="different">different</option>
4262 </param>
4263 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4264 </when>
4265 <when value="sequence_md5">
4266 <param name="operation" type="select" label="Operator">
4267 <option value="equal">equal</option>
4268 <option value="different">different</option>
4269 </param>
4270 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4271 </when>
4272 <when value="tax_division">
4273 <param name="operation" type="select" label="Operator">
4274 <option value="equal">equal</option>
4275 <option value="different">different</option>
4276 </param>
4277 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4278 </when>
4279 <when value="old_locus_tag">
4280 <param name="operation" type="select" label="Operator">
4281 <option value="equal">equal</option>
4282 <option value="different">different</option>
4283 </param>
4284 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4285 </when>
4286 <when value="specimen_voucher">
4287 <param name="operation" type="select" label="Operator">
4288 <option value="equal">equal</option>
4289 <option value="different">different</option>
4290 </param>
4291 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4292 </when>
4293 <when value="altitude">
4294 <param name="operation" type="select" label="Operator">
4295 <option value="equal">equal</option>
4296 <option value="different">different</option>
4297 <option value="lower">lower</option>
4298 <option value="equal or lower">equal or lower</option>
4299 <option value="higher">higher</option>
4300 <option value="equal or higher">equal or higher</option>
4301 </param>
4302 <param name="value" type="float" value="" label="Any integer"/>
4303 </when>
4304 <when value="dev_stage">
4305 <param name="operation" type="select" label="Operator">
4306 <option value="equal">equal</option>
4307 <option value="different">different</option>
4308 </param>
4309 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4310 </when>
4311 <when value="isolate">
4312 <param name="operation" type="select" label="Operator">
4313 <option value="equal">equal</option>
4314 <option value="different">different</option>
4315 </param>
4316 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4317 </when>
4318 <when value="ec_number">
4319 <param name="operation" type="select" label="Operator">
4320 <option value="equal">equal</option>
4321 <option value="different">different</option>
4322 </param>
4323 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4324 </when>
4325 <when value="note">
4326 <param name="operation" type="select" label="Operator">
4327 <option value="equal">equal</option>
4328 <option value="different">different</option>
4329 </param>
4330 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4331 </when>
4332 <when value="experiment">
4333 <param name="operation" type="select" label="Operator">
4334 <option value="equal">equal</option>
4335 <option value="different">different</option>
4336 </param>
4337 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4338 </when>
4339 <when value="location">
4340 <conditional name="op">
4341 <param name="operation" type="select" label="Operation">
4342 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
4343 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
4344 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
4345 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
4346 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
4347 <option value="geo_point">An exact lat/lon position</option>
4348 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
4349 </param>
4350 <when value="geo_box2">
4351 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
4352 </when>
4353 <when value="geo_box1">
4354 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
4355 </when>
4356 <when value="geo_circ">
4357 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
4358 </when>
4359 <when value="geo_lat">
4360 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
4361 </when>
4362 <when value="geo_south">
4363 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
4364 </when>
4365 <when value="geo_point">
4366 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
4367 </when>
4368 <when value="geo_north">
4369 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
4370 </when>
4371 </conditional>
4372 </when>
4373 <when value="collection_date">
4374 <param name="operation" type="select" label="Operator">
4375 <option value="equal">equal</option>
4376 <option value="different">different</option>
4377 <option value="lower">lower</option>
4378 <option value="equal or lower">equal or lower</option>
4379 <option value="higher">higher</option>
4380 <option value="equal or higher">equal or higher</option>
4381 </param>
4382 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
4383 </when>
4384 <when value="allele">
4385 <param name="operation" type="select" label="Operator">
4386 <option value="equal">equal</option>
4387 <option value="different">different</option>
4388 </param>
4389 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4390 </when>
4391 <when value="protein_id">
4392 <param name="operation" type="select" label="Operator">
4393 <option value="equal">equal</option>
4394 <option value="different">different</option>
4395 </param>
4396 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4397 </when>
4398 <when value="partial">
4399 <param name="operation" type="select" label="Operator">
4400 <option value="equal">equal</option>
4401 </param>
4402 <param name="value" type="select" label="Value">
4403 <option value="yes">yes</option>
4404 <option value="true">true</option>
4405 <option value="no">no</option>
4406 <option value="false">false</option>
4407 </param>
4408 </when>
4409 <when value="artificial_location">
4410 <param name="operation" type="select" label="Operator">
4411 <option value="equal">equal</option>
4412 <option value="different">different</option>
4413 </param>
4414 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4415 </when>
4416 <when value="function">
4417 <param name="operation" type="select" label="Operator">
4418 <option value="equal">equal</option>
4419 <option value="different">different</option>
4420 </param>
4421 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4422 </when>
4423 <when value="map">
4424 <param name="operation" type="select" label="Operator">
4425 <option value="equal">equal</option>
4426 <option value="different">different</option>
4427 </param>
4428 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4429 </when>
4430 <when value="product">
4431 <param name="operation" type="select" label="Operator">
4432 <option value="equal">equal</option>
4433 <option value="different">different</option>
4434 </param>
4435 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4436 </when>
4437 <when value="description">
4438 <param name="operation" type="select" label="Operator">
4439 <option value="equal">equal</option>
4440 <option value="different">different</option>
4441 </param>
4442 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4443 </when>
4444 <when value="cell_line">
4445 <param name="operation" type="select" label="Operator">
4446 <option value="equal">equal</option>
4447 <option value="different">different</option>
4448 </param>
4449 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4450 </when>
4451 <when value="gene_synonym">
4452 <param name="operation" type="select" label="Operator">
4453 <option value="equal">equal</option>
4454 <option value="different">different</option>
4455 </param>
4456 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4457 </when>
4458 <when value="ecotype">
4459 <param name="operation" type="select" label="Operator">
4460 <option value="equal">equal</option>
4461 <option value="different">different</option>
4462 </param>
4463 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4464 </when>
4465 <when value="exception">
4466 <param name="operation" type="select" label="Operator">
4467 <option value="equal">equal</option>
4468 <option value="different">different</option>
4469 </param>
4470 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4471 </when>
4472 <when value="accession">
4473 <param name="operation" type="select" label="Operator">
4474 <option value="equal">equal</option>
4475 <option value="different">different</option>
4476 </param>
4477 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4478 </when>
4479 <when value="isolation_source">
4480 <param name="operation" type="select" label="Operator">
4481 <option value="equal">equal</option>
4482 <option value="different">different</option>
4483 </param>
4484 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4485 </when>
4486 <when value="mating_type">
4487 <param name="operation" type="select" label="Operator">
4488 <option value="equal">equal</option>
4489 <option value="different">different</option>
4490 </param>
4491 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4492 </when>
4493 <when value="tissue_type">
4494 <param name="operation" type="select" label="Operator">
4495 <option value="equal">equal</option>
4496 <option value="different">different</option>
4497 </param>
4498 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4499 </when>
4500 <when value="sub_strain">
4501 <param name="operation" type="select" label="Operator">
4502 <option value="equal">equal</option>
4503 <option value="different">different</option>
4504 </param>
4505 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4506 </when>
4507 <when value="tissue_lib">
4508 <param name="operation" type="select" label="Operator">
4509 <option value="equal">equal</option>
4510 <option value="different">different</option>
4511 </param>
4512 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4513 </when>
4514 <when value="cultivar">
4515 <param name="operation" type="select" label="Operator">
4516 <option value="equal">equal</option>
4517 <option value="different">different</option>
4518 </param>
4519 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4520 </when>
4521 <when value="base_count">
4522 <param name="operation" type="select" label="Operator">
4523 <option value="equal">equal</option>
4524 <option value="different">different</option>
4525 <option value="lower">lower</option>
4526 <option value="equal or lower">equal or lower</option>
4527 <option value="higher">higher</option>
4528 <option value="equal or higher">equal or higher</option>
4529 </param>
4530 <param name="value" type="float" value="" label="Any integer"/>
4531 </when>
4532 <when value="topology">
4533 <param name="operation" type="select" label="Operator">
4534 <option value="equal">equal</option>
4535 <option value="different">different</option>
4536 </param>
4537 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4538 </when>
4539 <when value="sub_species">
4540 <param name="operation" type="select" label="Operator">
4541 <option value="equal">equal</option>
4542 <option value="different">different</option>
4543 </param>
4544 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4545 </when>
4546 <when value="first_public">
4547 <param name="operation" type="select" label="Operator">
4548 <option value="equal">equal</option>
4549 <option value="different">different</option>
4550 <option value="lower">lower</option>
4551 <option value="equal or lower">equal or lower</option>
4552 <option value="higher">higher</option>
4553 <option value="equal or higher">equal or higher</option>
4554 </param>
4555 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
4556 </when>
4557 <when value="strain">
4558 <param name="operation" type="select" label="Operator">
4559 <option value="equal">equal</option>
4560 <option value="different">different</option>
4561 </param>
4562 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4563 </when>
4564 <when value="country">
4565 <param name="operation" type="select" label="Operator">
4566 <option value="equal">equal</option>
4567 <option value="different">different</option>
4568 </param>
4569 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4570 </when>
4571 <when value="variety">
4572 <param name="operation" type="select" label="Operator">
4573 <option value="equal">equal</option>
4574 <option value="different">different</option>
4575 </param>
4576 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4577 </when>
4578 <when value="pseudo">
4579 <param name="operation" type="select" label="Operator">
4580 <option value="equal">equal</option>
4581 </param>
4582 <param name="value" type="select" label="Value">
4583 <option value="yes">yes</option>
4584 <option value="true">true</option>
4585 <option value="no">no</option>
4586 <option value="false">false</option>
4587 </param>
4588 </when>
4589 <when value="environmental_sample">
4590 <param name="operation" type="select" label="Operator">
4591 <option value="equal">equal</option>
4592 </param>
4593 <param name="value" type="select" label="Value">
4594 <option value="yes">yes</option>
4595 <option value="true">true</option>
4596 <option value="no">no</option>
4597 <option value="false">false</option>
4598 </param>
4599 </when>
4600 <when value="transl_table">
4601 <param name="operation" type="select" label="Operator">
4602 <option value="equal">equal</option>
4603 <option value="different">different</option>
4604 </param>
4605 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4606 </when>
4607 <when value="organelle">
4608 <param name="operation" type="select" label="Operator">
4609 <option value="equal">equal</option>
4610 <option value="different">different</option>
4611 </param>
4612 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4613 </when>
4614 <when value="ribosomal_slippage">
4615 <param name="operation" type="select" label="Operator">
4616 <option value="equal">equal</option>
4617 </param>
4618 <param name="value" type="select" label="Value">
4619 <option value="yes">yes</option>
4620 <option value="true">true</option>
4621 <option value="no">no</option>
4622 <option value="false">false</option>
4623 </param>
4624 </when>
4625 <when value="serovar">
4626 <param name="operation" type="select" label="Operator">
4627 <option value="equal">equal</option>
4628 <option value="different">different</option>
4629 </param>
4630 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4631 </when>
4632 <when value="keywords">
4633 <param name="operation" type="select" label="Operator">
4634 <option value="equal">equal</option>
4635 <option value="different">different</option>
4636 </param>
4637 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4638 </when>
4639 <when value="dataclass">
4640 <param name="operation" type="select" label="Operator">
4641 <option value="equal">equal</option>
4642 <option value="different">different</option>
4643 </param>
4644 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4645 </when>
4646 <when value="gene">
4647 <param name="operation" type="select" label="Operator">
4648 <option value="equal">equal</option>
4649 <option value="different">different</option>
4650 </param>
4651 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4652 </when>
4653 <when value="codon_start">
4654 <param name="operation" type="select" label="Operator">
4655 <option value="equal">equal</option>
4656 <option value="different">different</option>
4657 </param>
4658 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4659 </when>
4660 <when value="culture_collection">
4661 <param name="operation" type="select" label="Operator">
4662 <option value="equal">equal</option>
4663 <option value="different">different</option>
4664 </param>
4665 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4666 </when>
4667 </conditional>
4668 </repeat>
4669 <conditional name="display_opt">
4670 <param argument="--display" type="select" label="Display option to specify the display format">
4671 <expand macro="display_options"/>
4672 </param>
4673 <when value="xml">
4674 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4675 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4676 </when>
4677 <when value="text">
4678 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4679 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4680 </when>
4681 <when value="fastq"/>
4682 <when value="html">
4683 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4684 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4685 </when>
4686 <when value="report">
4687 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
4688 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
4689 <param argument="--fields" type="select" multiple="true" label="Fields to return">
4690 <option value="accession">accession</option>
4691 <option value="base_count">base_count</option>
4692 <option value="bio_material">bio_material</option>
4693 <option value="cell_line">cell_line</option>
4694 <option value="cell_type">cell_type</option>
4695 <option value="collected_by">collected_by</option>
4696 <option value="collection_date">collection_date</option>
4697 <option value="country">country</option>
4698 <option value="cultivar">cultivar</option>
4699 <option value="culture_collection">culture_collection</option>
4700 <option value="dataclass">dataclass</option>
4701 <option value="description">description</option>
4702 <option value="dev_stage">dev_stage</option>
4703 <option value="ecotype">ecotype</option>
4704 <option value="environmental_sample">environmental_sample</option>
4705 <option value="first_public">first_public</option>
4706 <option value="germline">germline</option>
4707 <option value="host">host</option>
4708 <option value="identified_by">identified_by</option>
4709 <option value="isolate">isolate</option>
4710 <option value="isolation_source">isolation_source</option>
4711 <option value="keywords">keywords</option>
4712 <option value="lab_host">lab_host</option>
4713 <option value="last_updated">last_updated</option>
4714 <option value="location">location</option>
4715 <option value="mating_type">mating_type</option>
4716 <option value="mol_type">mol_type</option>
4717 <option value="organelle">organelle</option>
4718 <option value="serotype">serotype</option>
4719 <option value="serovar">serovar</option>
4720 <option value="sex">sex</option>
4721 <option value="submitted_sex">submitted_sex</option>
4722 <option value="specimen_voucher">specimen_voucher</option>
4723 <option value="strain">strain</option>
4724 <option value="sub_species">sub_species</option>
4725 <option value="sub_strain">sub_strain</option>
4726 <option value="tax_division">tax_division</option>
4727 <option value="tissue_lib">tissue_lib</option>
4728 <option value="tissue_type">tissue_type</option>
4729 <option value="variety">variety</option>
4730 <option value="allele">allele</option>
4731 <option value="artificial_location">artificial_location</option>
4732 <option value="codon_start">codon_start</option>
4733 <option value="ec_number">ec_number</option>
4734 <option value="exception">exception</option>
4735 <option value="experiment">experiment</option>
4736 <option value="function">function</option>
4737 <option value="topology">topology</option>
4738 <option value="gene">gene</option>
4739 <option value="gene_synonym">gene_synonym</option>
4740 <option value="inference">inference</option>
4741 <option value="locus_tag">locus_tag</option>
4742 <option value="map">map</option>
4743 <option value="note">note</option>
4744 <option value="old_locus_tag">old_locus_tag</option>
4745 <option value="operon">operon</option>
4746 <option value="partial">partial</option>
4747 <option value="product">product</option>
4748 <option value="protein_id">protein_id</option>
4749 <option value="pseudo">pseudo</option>
4750 <option value="pseudo_gene">pseudo_gene</option>
4751 <option value="ribosomal_slippage">ribosomal_slippage</option>
4752 <option value="standard_name">standard_name</option>
4753 <option value="trans_splicing">trans_splicing</option>
4754 <option value="transl_except">transl_except</option>
4755 <option value="transl_table">transl_table</option>
4756 <option value="tax_id">tax_id</option>
4757 <option value="scientific_name">scientific_name</option>
4758 <option value="parent_accession">parent_accession</option>
4759 <option value="altitude">altitude</option>
4760 <option value="haplotype">haplotype</option>
4761 <option value="sequence_md5">sequence_md5</option>
4762 </param>
4763 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
4764 <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option>
4765 <option value="mol_type">in vivo molecule type of the sequence</option>
4766 <option value="last_updated">date when last updated</option>
4767 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
4768 <option value="transl_except">a single codon translation that does not conform to genetic code</option>
4769 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
4770 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
4771 <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option>
4772 <option value="sex">sex of the organism from which the sample was obtained</option>
4773 <option value="pseudo_gene">indicates that this feature is a pseudogene</option>
4774 <option value="standard_name">accepted standard name for a feature</option>
4775 <option value="collected_by">name of the person who collected the specimen</option>
4776 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
4777 <option value="cell_type">cell type from which the sample was obtained</option>
4778 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
4779 <option value="inference">a structured description of non-experimental evidence</option>
4780 <option value="bio_material">identifier for biological material including institute and collection code</option>
4781 <option value="parent_accession">parent sequence accession number</option>
4782 <option value="identified_by">name of the taxonomist who identified the specimen</option>
4783 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
4784 <option value="sequence_md5"></option>
4785 <option value="tax_division">taxonomic division</option>
4786 <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
4787 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
4788 <option value="altitude">Altitude (m)</option>
4789 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
4790 <option value="isolate">individual isolate from which sample was obtained</option>
4791 <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option>
4792 <option value="note">any comment or additional information</option>
4793 <option value="experiment">a brief description of the nature of the experimental evidence</option>
4794 <option value="location">geographic location of isolation of the sample</option>
4795 <option value="collection_date">date that the specimen was collected</option>
4796 <option value="allele">name of the allele for the given gene</option>
4797 <option value="protein_id">a stable protein identifier issued by INSDC</option>
4798 <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option>
4799 <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option>
4800 <option value="function">function attributed to a sequence</option>
4801 <option value="map">genomic map position of feature</option>
4802 <option value="product">name of the product associated with the feature</option>
4803 <option value="description">brief sequence description</option>
4804 <option value="cell_line">cell line from which the sample was obtained</option>
4805 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
4806 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
4807 <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option>
4808 <option value="accession">accession number</option>
4809 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
4810 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
4811 <option value="tissue_type">tissue type from which the sample was obtained</option>
4812 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
4813 <option value="tissue_lib">tissue library from which sample was obtained</option>
4814 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
4815 <option value="base_count">number of base pairs</option>
4816 <option value="topology">sequence topology: circular or linear</option>
4817 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
4818 <option value="first_public">date when made public</option>
4819 <option value="strain">strain from which sample was obtained</option>
4820 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
4821 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
4822 <option value="pseudo">the feature is non-functional</option>
4823 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
4824 <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option>
4825 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
4826 <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option>
4827 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
4828 <option value="keywords">keywords associated with sequence</option>
4829 <option value="dataclass">sequence data class</option>
4830 <option value="gene">symbol of the gene corresponding to a sequence region</option>
4831 <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option>
4832 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
4833 </param>
4834 </when>
4835 <when value="fasta"/>
4836 </conditional>
4837 </when>
4838 <when value="sample">
4839 <repeat name="queries" title="Add a query">
4840 <param name="combination_operation" type="select" label="Combination operation">
4841 <option value="AND">AND</option>
4842 <option value="OR">OR</option>
4843 <option value="NOT">NOT</option>
4844 </param>
4845 <conditional name="filter_field">
4846 <param name="field" type="select" label="Field to query">
4847 <option value="secondary_sample_accession">secondary sample accession number</option>
4848 <option value="environment_material">Environment (Material)</option>
4849 <option value="host_sex">physical sex of the host</option>
4850 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
4851 <option value="center_name">Submitting center</option>
4852 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
4853 <option value="sex">sex of the organism from which the sample was obtained</option>
4854 <option value="host_phenotype">phenotype of host</option>
4855 <option value="sampling_site">the site/station where this sample was collection</option>
4856 <option value="sequencing_method">sequencing method used</option>
4857 <option value="cell_line">cell line from which the sample was obtained</option>
4858 <option value="bio_material">identifier for biological material including institute and collection code</option>
4859 <option value="target_gene">targeted gene or locus name for marker gene studies</option>
4860 <option value="experimental_factor">variable aspects of the experimental design</option>
4861 <option value="identified_by">name of the taxonomist who identified the specimen</option>
4862 <option value="cell_type">cell type from which the sample was obtained</option>
4863 <option value="temperature">Temperature (C)</option>
4864 <option value="sampling_platform">the large infrastructure from which this sample was collected</option>
4865 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
4866 <option value="collection_date">date that the specimen was collected</option>
4867 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
4868 <option value="altitude">Altitude (m)</option>
4869 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
4870 <option value="isolate">individual isolate from which sample was obtained</option>
4871 <option value="investigation_type">the study type targeted by the sequencing</option>
4872 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
4873 <option value="protocol_label">the protocol used to produce the sample</option>
4874 <option value="location">geographic location of isolation of the sample</option>
4875 <option value="host_genotype">genotype of host</option>
4876 <option value="ph">pH</option>
4877 <option value="broker_name">broker name</option>
4878 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
4879 <option value="project_name">name of the project within which the sequencing was organized</option>
4880 <option value="elevation">Elevation (m)</option>
4881 <option value="description">brief sequence description</option>
4882 <option value="sample_alias">submitter's name for the sample</option>
4883 <option value="checklist">checklist name (or ID)</option>
4884 <option value="sampling_campaign">the activity within which this sample was collected</option>
4885 <option value="accession">accession number</option>
4886 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
4887 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
4888 <option value="tissue_type">tissue type from which the sample was obtained</option>
4889 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
4890 <option value="tissue_lib">tissue library from which sample was obtained</option>
4891 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
4892 <option value="environment_biome">Environment (Biome)</option>
4893 <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option>
4894 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
4895 <option value="first_public">date when made public</option>
4896 <option value="environment_feature">Environment (Feature)</option>
4897 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
4898 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
4899 <option value="collected_by">name of the person who collected the specimen</option>
4900 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
4901 <option value="salinity">Salinity (PSU)</option>
4902 <option value="host_status">condition of host (eg. diseased or healthy)</option>
4903 <option value="strain">strain from which sample was obtained</option>
4904 <option value="depth">Depth (m)</option>
4905 <option value="host_tax_id">NCBI taxon id of the host</option>
4906 <option value="host_body_site">name of body site from where the sample was obtained</option>
4907 <option value="host_growth_conditions">literature reference giving growth conditions of the host</option>
4908 <option value="sample_collection">the method or deviced employed for collecting the sample</option>
4909 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
4910 </param>
4911 <when value="secondary_sample_accession">
4912 <param name="operation" type="select" label="Operator">
4913 <option value="equal">equal</option>
4914 <option value="different">different</option>
4915 </param>
4916 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4917 </when>
4918 <when value="environment_material">
4919 <param name="operation" type="select" label="Operator">
4920 <option value="equal">equal</option>
4921 <option value="different">different</option>
4922 </param>
4923 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4924 </when>
4925 <when value="host_sex">
4926 <param name="operation" type="select" label="Operator">
4927 <option value="equal">equal</option>
4928 <option value="different">different</option>
4929 </param>
4930 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4931 </when>
4932 <when value="ecotype">
4933 <param name="operation" type="select" label="Operator">
4934 <option value="equal">equal</option>
4935 <option value="different">different</option>
4936 </param>
4937 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4938 </when>
4939 <when value="center_name">
4940 <param name="operation" type="select" label="Operator">
4941 <option value="equal">equal</option>
4942 <option value="different">different</option>
4943 </param>
4944 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4945 </when>
4946 <when value="serotype">
4947 <param name="operation" type="select" label="Operator">
4948 <option value="equal">equal</option>
4949 <option value="different">different</option>
4950 </param>
4951 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4952 </when>
4953 <when value="sex">
4954 <param name="operation" type="select" label="Operator">
4955 <option value="equal">equal</option>
4956 <option value="different">different</option>
4957 </param>
4958 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
4959 </when>
4960 <when value="host_phenotype">
4961 <param name="operation" type="select" label="Operator">
4962 <option value="equal">equal</option>
4963 <option value="different">different</option>
4964 </param>
4965 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4966 </when>
4967 <when value="sampling_site">
4968 <param name="operation" type="select" label="Operator">
4969 <option value="equal">equal</option>
4970 <option value="different">different</option>
4971 </param>
4972 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4973 </when>
4974 <when value="sequencing_method">
4975 <param name="operation" type="select" label="Operator">
4976 <option value="equal">equal</option>
4977 <option value="different">different</option>
4978 </param>
4979 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4980 </when>
4981 <when value="cell_line">
4982 <param name="operation" type="select" label="Operator">
4983 <option value="equal">equal</option>
4984 <option value="different">different</option>
4985 </param>
4986 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4987 </when>
4988 <when value="bio_material">
4989 <param name="operation" type="select" label="Operator">
4990 <option value="equal">equal</option>
4991 <option value="different">different</option>
4992 </param>
4993 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
4994 </when>
4995 <when value="target_gene">
4996 <param name="operation" type="select" label="Operator">
4997 <option value="equal">equal</option>
4998 <option value="different">different</option>
4999 </param>
5000 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5001 </when>
5002 <when value="experimental_factor">
5003 <param name="operation" type="select" label="Operator">
5004 <option value="equal">equal</option>
5005 <option value="different">different</option>
5006 </param>
5007 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5008 </when>
5009 <when value="identified_by">
5010 <param name="operation" type="select" label="Operator">
5011 <option value="equal">equal</option>
5012 <option value="different">different</option>
5013 </param>
5014 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5015 </when>
5016 <when value="cell_type">
5017 <param name="operation" type="select" label="Operator">
5018 <option value="equal">equal</option>
5019 <option value="different">different</option>
5020 </param>
5021 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5022 </when>
5023 <when value="temperature">
5024 <param name="operation" type="select" label="Operator">
5025 <option value="equal">equal</option>
5026 <option value="different">different</option>
5027 <option value="lower">lower</option>
5028 <option value="equal or lower">equal or lower</option>
5029 <option value="higher">higher</option>
5030 <option value="equal or higher">equal or higher</option>
5031 </param>
5032 <param name="value" type="float" value="" label="Any integer"/>
5033 </when>
5034 <when value="sampling_platform">
5035 <param name="operation" type="select" label="Operator">
5036 <option value="equal">equal</option>
5037 <option value="different">different</option>
5038 </param>
5039 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5040 </when>
5041 <when value="variety">
5042 <param name="operation" type="select" label="Operator">
5043 <option value="equal">equal</option>
5044 <option value="different">different</option>
5045 </param>
5046 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5047 </when>
5048 <when value="collection_date">
5049 <param name="operation" type="select" label="Operator">
5050 <option value="equal">equal</option>
5051 <option value="different">different</option>
5052 <option value="lower">lower</option>
5053 <option value="equal or lower">equal or lower</option>
5054 <option value="higher">higher</option>
5055 <option value="equal or higher">equal or higher</option>
5056 </param>
5057 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
5058 </when>
5059 <when value="specimen_voucher">
5060 <param name="operation" type="select" label="Operator">
5061 <option value="equal">equal</option>
5062 <option value="different">different</option>
5063 </param>
5064 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5065 </when>
5066 <when value="altitude">
5067 <param name="operation" type="select" label="Operator">
5068 <option value="equal">equal</option>
5069 <option value="different">different</option>
5070 <option value="lower">lower</option>
5071 <option value="equal or lower">equal or lower</option>
5072 <option value="higher">higher</option>
5073 <option value="equal or higher">equal or higher</option>
5074 </param>
5075 <param name="value" type="float" value="" label="Any integer"/>
5076 </when>
5077 <when value="dev_stage">
5078 <param name="operation" type="select" label="Operator">
5079 <option value="equal">equal</option>
5080 <option value="different">different</option>
5081 </param>
5082 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5083 </when>
5084 <when value="isolate">
5085 <param name="operation" type="select" label="Operator">
5086 <option value="equal">equal</option>
5087 <option value="different">different</option>
5088 </param>
5089 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5090 </when>
5091 <when value="investigation_type">
5092 <param name="operation" type="select" label="Operator">
5093 <option value="equal">equal</option>
5094 <option value="different">different</option>
5095 </param>
5096 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5097 </when>
5098 <when value="serovar">
5099 <param name="operation" type="select" label="Operator">
5100 <option value="equal">equal</option>
5101 <option value="different">different</option>
5102 </param>
5103 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5104 </when>
5105 <when value="protocol_label">
5106 <param name="operation" type="select" label="Operator">
5107 <option value="equal">equal</option>
5108 <option value="different">different</option>
5109 </param>
5110 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5111 </when>
5112 <when value="location">
5113 <conditional name="op">
5114 <param name="operation" type="select" label="Operation">
5115 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
5116 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
5117 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
5118 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
5119 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
5120 <option value="geo_point">An exact lat/lon position</option>
5121 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
5122 </param>
5123 <when value="geo_box2">
5124 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
5125 </when>
5126 <when value="geo_box1">
5127 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
5128 </when>
5129 <when value="geo_circ">
5130 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
5131 </when>
5132 <when value="geo_lat">
5133 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
5134 </when>
5135 <when value="geo_south">
5136 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
5137 </when>
5138 <when value="geo_point">
5139 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
5140 </when>
5141 <when value="geo_north">
5142 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
5143 </when>
5144 </conditional>
5145 </when>
5146 <when value="host_genotype">
5147 <param name="operation" type="select" label="Operator">
5148 <option value="equal">equal</option>
5149 <option value="different">different</option>
5150 </param>
5151 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5152 </when>
5153 <when value="ph">
5154 <param name="operation" type="select" label="Operator">
5155 <option value="equal">equal</option>
5156 <option value="different">different</option>
5157 <option value="lower">lower</option>
5158 <option value="equal or lower">equal or lower</option>
5159 <option value="higher">higher</option>
5160 <option value="equal or higher">equal or higher</option>
5161 </param>
5162 <param name="value" type="float" value="" label="Any integer"/>
5163 </when>
5164 <when value="broker_name">
5165 <param name="operation" type="select" label="Operator">
5166 <option value="equal">equal</option>
5167 <option value="different">different</option>
5168 </param>
5169 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5170 </when>
5171 <when value="germline">
5172 <param name="operation" type="select" label="Operator">
5173 <option value="equal">equal</option>
5174 </param>
5175 <param name="value" type="select" label="Value">
5176 <option value="yes">yes</option>
5177 <option value="true">true</option>
5178 <option value="no">no</option>
5179 <option value="false">false</option>
5180 </param>
5181 </when>
5182 <when value="project_name">
5183 <param name="operation" type="select" label="Operator">
5184 <option value="equal">equal</option>
5185 <option value="different">different</option>
5186 </param>
5187 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5188 </when>
5189 <when value="elevation">
5190 <param name="operation" type="select" label="Operator">
5191 <option value="equal">equal</option>
5192 <option value="different">different</option>
5193 <option value="lower">lower</option>
5194 <option value="equal or lower">equal or lower</option>
5195 <option value="higher">higher</option>
5196 <option value="equal or higher">equal or higher</option>
5197 </param>
5198 <param name="value" type="float" value="" label="Any integer"/>
5199 </when>
5200 <when value="description">
5201 <param name="operation" type="select" label="Operator">
5202 <option value="equal">equal</option>
5203 <option value="different">different</option>
5204 </param>
5205 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5206 </when>
5207 <when value="sample_alias">
5208 <param name="operation" type="select" label="Operator">
5209 <option value="equal">equal</option>
5210 <option value="different">different</option>
5211 </param>
5212 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5213 </when>
5214 <when value="checklist">
5215 <param name="operation" type="select" label="Operator">
5216 <option value="equal">equal</option>
5217 <option value="different">different</option>
5218 </param>
5219 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5220 </when>
5221 <when value="sampling_campaign">
5222 <param name="operation" type="select" label="Operator">
5223 <option value="equal">equal</option>
5224 <option value="different">different</option>
5225 </param>
5226 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5227 </when>
5228 <when value="accession">
5229 <param name="operation" type="select" label="Operator">
5230 <option value="equal">equal</option>
5231 <option value="different">different</option>
5232 </param>
5233 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5234 </when>
5235 <when value="isolation_source">
5236 <param name="operation" type="select" label="Operator">
5237 <option value="equal">equal</option>
5238 <option value="different">different</option>
5239 </param>
5240 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5241 </when>
5242 <when value="mating_type">
5243 <param name="operation" type="select" label="Operator">
5244 <option value="equal">equal</option>
5245 <option value="different">different</option>
5246 </param>
5247 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5248 </when>
5249 <when value="tissue_type">
5250 <param name="operation" type="select" label="Operator">
5251 <option value="equal">equal</option>
5252 <option value="different">different</option>
5253 </param>
5254 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5255 </when>
5256 <when value="sub_strain">
5257 <param name="operation" type="select" label="Operator">
5258 <option value="equal">equal</option>
5259 <option value="different">different</option>
5260 </param>
5261 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5262 </when>
5263 <when value="tissue_lib">
5264 <param name="operation" type="select" label="Operator">
5265 <option value="equal">equal</option>
5266 <option value="different">different</option>
5267 </param>
5268 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5269 </when>
5270 <when value="cultivar">
5271 <param name="operation" type="select" label="Operator">
5272 <option value="equal">equal</option>
5273 <option value="different">different</option>
5274 </param>
5275 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5276 </when>
5277 <when value="environment_biome">
5278 <param name="operation" type="select" label="Operator">
5279 <option value="equal">equal</option>
5280 <option value="different">different</option>
5281 </param>
5282 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5283 </when>
5284 <when value="environmental_package">
5285 <param name="operation" type="select" label="Operator">
5286 <option value="equal">equal</option>
5287 <option value="different">different</option>
5288 </param>
5289 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5290 </when>
5291 <when value="sub_species">
5292 <param name="operation" type="select" label="Operator">
5293 <option value="equal">equal</option>
5294 <option value="different">different</option>
5295 </param>
5296 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5297 </when>
5298 <when value="first_public">
5299 <param name="operation" type="select" label="Operator">
5300 <option value="equal">equal</option>
5301 <option value="different">different</option>
5302 <option value="lower">lower</option>
5303 <option value="equal or lower">equal or lower</option>
5304 <option value="higher">higher</option>
5305 <option value="equal or higher">equal or higher</option>
5306 </param>
5307 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
5308 </when>
5309 <when value="environment_feature">
5310 <param name="operation" type="select" label="Operator">
5311 <option value="equal">equal</option>
5312 <option value="different">different</option>
5313 </param>
5314 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5315 </when>
5316 <when value="host">
5317 <param name="operation" type="select" label="Operator">
5318 <option value="equal">equal</option>
5319 <option value="different">different</option>
5320 </param>
5321 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5322 </when>
5323 <when value="country">
5324 <param name="operation" type="select" label="Operator">
5325 <option value="equal">equal</option>
5326 <option value="different">different</option>
5327 </param>
5328 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5329 </when>
5330 <when value="collected_by">
5331 <param name="operation" type="select" label="Operator">
5332 <option value="equal">equal</option>
5333 <option value="different">different</option>
5334 </param>
5335 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5336 </when>
5337 <when value="environmental_sample">
5338 <param name="operation" type="select" label="Operator">
5339 <option value="equal">equal</option>
5340 </param>
5341 <param name="value" type="select" label="Value">
5342 <option value="yes">yes</option>
5343 <option value="true">true</option>
5344 <option value="no">no</option>
5345 <option value="false">false</option>
5346 </param>
5347 </when>
5348 <when value="salinity">
5349 <param name="operation" type="select" label="Operator">
5350 <option value="equal">equal</option>
5351 <option value="different">different</option>
5352 <option value="lower">lower</option>
5353 <option value="equal or lower">equal or lower</option>
5354 <option value="higher">higher</option>
5355 <option value="equal or higher">equal or higher</option>
5356 </param>
5357 <param name="value" type="float" value="" label="Any integer"/>
5358 </when>
5359 <when value="host_status">
5360 <param name="operation" type="select" label="Operator">
5361 <option value="equal">equal</option>
5362 <option value="different">different</option>
5363 </param>
5364 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5365 </when>
5366 <when value="strain">
5367 <param name="operation" type="select" label="Operator">
5368 <option value="equal">equal</option>
5369 <option value="different">different</option>
5370 </param>
5371 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5372 </when>
5373 <when value="depth">
5374 <param name="operation" type="select" label="Operator">
5375 <option value="equal">equal</option>
5376 <option value="different">different</option>
5377 <option value="lower">lower</option>
5378 <option value="equal or lower">equal or lower</option>
5379 <option value="higher">higher</option>
5380 <option value="equal or higher">equal or higher</option>
5381 </param>
5382 <param name="value" type="float" value="" label="Any integer"/>
5383 </when>
5384 <when value="host_tax_id">
5385 <param name="operation" type="select" label="Operator">
5386 <option value="equal">equal</option>
5387 <option value="different">different</option>
5388 <option value="lower">lower</option>
5389 <option value="equal or lower">equal or lower</option>
5390 <option value="higher">higher</option>
5391 <option value="equal or higher">equal or higher</option>
5392 </param>
5393 <param name="value" type="float" value="" label="Any integer"/>
5394 </when>
5395 <when value="host_body_site">
5396 <param name="operation" type="select" label="Operator">
5397 <option value="equal">equal</option>
5398 <option value="different">different</option>
5399 </param>
5400 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5401 </when>
5402 <when value="host_growth_conditions">
5403 <param name="operation" type="select" label="Operator">
5404 <option value="equal">equal</option>
5405 <option value="different">different</option>
5406 </param>
5407 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5408 </when>
5409 <when value="sample_collection">
5410 <param name="operation" type="select" label="Operator">
5411 <option value="equal">equal</option>
5412 <option value="different">different</option>
5413 </param>
5414 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5415 </when>
5416 <when value="culture_collection">
5417 <param name="operation" type="select" label="Operator">
5418 <option value="equal">equal</option>
5419 <option value="different">different</option>
5420 </param>
5421 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5422 </when>
5423 </conditional>
5424 </repeat>
5425 <conditional name="display_opt">
5426 <param argument="--display" type="select" label="Display option to specify the display format">
5427 <expand macro="display_options"/>
5428 </param>
5429 <when value="xml">
5430 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
5431 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
5432 </when>
5433 <when value="text">
5434 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
5435 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
5436 </when>
5437 <when value="fastq"/>
5438 <when value="html">
5439 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
5440 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
5441 </when>
5442 <when value="report">
5443 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
5444 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
5445 <param argument="--fields" type="select" multiple="true" label="Fields to return">
5446 <option value="accession">accession</option>
5447 <option value="secondary_sample_accession">secondary_sample_accession</option>
5448 <option value="bio_material">bio_material</option>
5449 <option value="cell_line">cell_line</option>
5450 <option value="cell_type">cell_type</option>
5451 <option value="collected_by">collected_by</option>
5452 <option value="collection_date">collection_date</option>
5453 <option value="country">country</option>
5454 <option value="cultivar">cultivar</option>
5455 <option value="culture_collection">culture_collection</option>
5456 <option value="description">description</option>
5457 <option value="dev_stage">dev_stage</option>
5458 <option value="ecotype">ecotype</option>
5459 <option value="environmental_sample">environmental_sample</option>
5460 <option value="first_public">first_public</option>
5461 <option value="germline">germline</option>
5462 <option value="identified_by">identified_by</option>
5463 <option value="isolate">isolate</option>
5464 <option value="isolation_source">isolation_source</option>
5465 <option value="location">location</option>
5466 <option value="mating_type">mating_type</option>
5467 <option value="serotype">serotype</option>
5468 <option value="serovar">serovar</option>
5469 <option value="sex">sex</option>
5470 <option value="submitted_sex">submitted_sex</option>
5471 <option value="specimen_voucher">specimen_voucher</option>
5472 <option value="strain">strain</option>
5473 <option value="sub_species">sub_species</option>
5474 <option value="sub_strain">sub_strain</option>
5475 <option value="tissue_lib">tissue_lib</option>
5476 <option value="tissue_type">tissue_type</option>
5477 <option value="variety">variety</option>
5478 <option value="tax_id">tax_id</option>
5479 <option value="scientific_name">scientific_name</option>
5480 <option value="sample_alias">sample_alias</option>
5481 <option value="checklist">checklist</option>
5482 <option value="center_name">center_name</option>
5483 <option value="depth">depth</option>
5484 <option value="elevation">elevation</option>
5485 <option value="altitude">altitude</option>
5486 <option value="environment_biome">environment_biome</option>
5487 <option value="environment_feature">environment_feature</option>
5488 <option value="environment_material">environment_material</option>
5489 <option value="temperature">temperature</option>
5490 <option value="salinity">salinity</option>
5491 <option value="sampling_campaign">sampling_campaign</option>
5492 <option value="sampling_site">sampling_site</option>
5493 <option value="sampling_platform">sampling_platform</option>
5494 <option value="protocol_label">protocol_label</option>
5495 <option value="project_name">project_name</option>
5496 <option value="host">host</option>
5497 <option value="host_tax_id">host_tax_id</option>
5498 <option value="host_status">host_status</option>
5499 <option value="host_sex">host_sex</option>
5500 <option value="submitted_host_sex">submitted_host_sex</option>
5501 <option value="host_body_site">host_body_site</option>
5502 <option value="host_gravidity">host_gravidity</option>
5503 <option value="host_phenotype">host_phenotype</option>
5504 <option value="host_genotype">host_genotype</option>
5505 <option value="host_growth_conditions">host_growth_conditions</option>
5506 <option value="environmental_package">environmental_package</option>
5507 <option value="investigation_type">investigation_type</option>
5508 <option value="experimental_factor">experimental_factor</option>
5509 <option value="sample_collection">sample_collection</option>
5510 <option value="sequencing_method">sequencing_method</option>
5511 <option value="target_gene">target_gene</option>
5512 <option value="ph">ph</option>
5513 <option value="broker_name">broker_name</option>
5514 </param>
5515 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
5516 <option value="secondary_sample_accession">secondary sample accession number</option>
5517 <option value="environment_material">Environment (Material)</option>
5518 <option value="host_sex">physical sex of the host</option>
5519 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
5520 <option value="center_name">Submitting center</option>
5521 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
5522 <option value="sex">sex of the organism from which the sample was obtained</option>
5523 <option value="host_phenotype">phenotype of host</option>
5524 <option value="sampling_site">the site/station where this sample was collection</option>
5525 <option value="sequencing_method">sequencing method used</option>
5526 <option value="cell_line">cell line from which the sample was obtained</option>
5527 <option value="bio_material">identifier for biological material including institute and collection code</option>
5528 <option value="target_gene">targeted gene or locus name for marker gene studies</option>
5529 <option value="experimental_factor">variable aspects of the experimental design</option>
5530 <option value="identified_by">name of the taxonomist who identified the specimen</option>
5531 <option value="cell_type">cell type from which the sample was obtained</option>
5532 <option value="temperature">Temperature (C)</option>
5533 <option value="sampling_platform">the large infrastructure from which this sample was collected</option>
5534 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
5535 <option value="collection_date">date that the specimen was collected</option>
5536 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
5537 <option value="altitude">Altitude (m)</option>
5538 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
5539 <option value="isolate">individual isolate from which sample was obtained</option>
5540 <option value="investigation_type">the study type targeted by the sequencing</option>
5541 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
5542 <option value="protocol_label">the protocol used to produce the sample</option>
5543 <option value="location">geographic location of isolation of the sample</option>
5544 <option value="host_genotype">genotype of host</option>
5545 <option value="ph">pH</option>
5546 <option value="broker_name">broker name</option>
5547 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
5548 <option value="project_name">name of the project within which the sequencing was organized</option>
5549 <option value="elevation">Elevation (m)</option>
5550 <option value="description">brief sequence description</option>
5551 <option value="sample_alias">submitter's name for the sample</option>
5552 <option value="checklist">checklist name (or ID)</option>
5553 <option value="sampling_campaign">the activity within which this sample was collected</option>
5554 <option value="accession">accession number</option>
5555 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
5556 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
5557 <option value="tissue_type">tissue type from which the sample was obtained</option>
5558 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
5559 <option value="tissue_lib">tissue library from which sample was obtained</option>
5560 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
5561 <option value="environment_biome">Environment (Biome)</option>
5562 <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option>
5563 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
5564 <option value="first_public">date when made public</option>
5565 <option value="environment_feature">Environment (Feature)</option>
5566 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
5567 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
5568 <option value="collected_by">name of the person who collected the specimen</option>
5569 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
5570 <option value="salinity">Salinity (PSU)</option>
5571 <option value="host_status">condition of host (eg. diseased or healthy)</option>
5572 <option value="strain">strain from which sample was obtained</option>
5573 <option value="depth">Depth (m)</option>
5574 <option value="host_tax_id">NCBI taxon id of the host</option>
5575 <option value="host_body_site">name of body site from where the sample was obtained</option>
5576 <option value="host_growth_conditions">literature reference giving growth conditions of the host</option>
5577 <option value="sample_collection">the method or deviced employed for collecting the sample</option>
5578 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
5579 </param>
5580 </when>
5581 <when value="fasta"/>
5582 </conditional>
5583 </when>
5584 <when value="environmental">
5585 <repeat name="queries" title="Add a query">
5586 <param name="combination_operation" type="select" label="Combination operation">
5587 <option value="AND">AND</option>
5588 <option value="OR">OR</option>
5589 <option value="NOT">NOT</option>
5590 </param>
5591 <conditional name="filter_field">
5592 <param name="field" type="select" label="Field to query">
5593 <option value="secondary_sample_accession">secondary sample accession number</option>
5594 <option value="environment_material">Environment (Material)</option>
5595 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
5596 <option value="event_label">label given to sampling event</option>
5597 <option value="center_name">Submitting center</option>
5598 <option value="accession">accession number</option>
5599 <option value="host_phenotype">phenotype of host</option>
5600 <option value="cell_line">cell line from which the sample was obtained</option>
5601 <option value="bio_material">identifier for biological material including institute and collection code</option>
5602 <option value="target_gene">targeted gene or locus name for marker gene studies</option>
5603 <option value="experimental_factor">variable aspects of the experimental design</option>
5604 <option value="identified_by">name of the taxonomist who identified the specimen</option>
5605 <option value="temperature">Temperature (C)</option>
5606 <option value="sampling_platform">the large infrastructure from which this sample was collected</option>
5607 <option value="collected_by">name of the person who collected the specimen</option>
5608 <option value="collection_date">date that the specimen was collected</option>
5609 <option value="altitude">Altitude (m)</option>
5610 <option value="host_sex">physical sex of the host</option>
5611 <option value="investigation_type">the study type targeted by the sequencing</option>
5612 <option value="location">geographic location of isolation of the sample</option>
5613 <option value="host_genotype">genotype of host</option>
5614 <option value="ph">pH</option>
5615 <option value="broker_name">broker name</option>
5616 <option value="project_name">name of the project within which the sequencing was organized</option>
5617 <option value="elevation">Elevation (m)</option>
5618 <option value="description">brief sequence description</option>
5619 <option value="sample_alias">submitter's name for the sample</option>
5620 <option value="checklist">checklist name (or ID)</option>
5621 <option value="sampling_campaign">the activity within which this sample was collected</option>
5622 <option value="protocol_label">the protocol used to produce the sample</option>
5623 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
5624 <option value="sampling_site">the site/station where this sample was collection</option>
5625 <option value="host_tax_id">NCBI taxon id of the host</option>
5626 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
5627 <option value="environment_biome">Environment (Biome)</option>
5628 <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option>
5629 <option value="marine_region">geographical origin of the sample as defined by the marine region</option>
5630 <option value="first_public">date when made public</option>
5631 <option value="environment_feature">Environment (Feature)</option>
5632 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
5633 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
5634 <option value="salinity">Salinity (PSU)</option>
5635 <option value="host_status">condition of host (eg. diseased or healthy)</option>
5636 <option value="strain">strain from which sample was obtained</option>
5637 <option value="depth">Depth (m)</option>
5638 <option value="tissue_type">tissue type from which the sample was obtained</option>
5639 <option value="host_body_site">name of body site from where the sample was obtained</option>
5640 <option value="host_growth_conditions">literature reference giving growth conditions of the host</option>
5641 <option value="sample_collection">the method or deviced employed for collecting the sample</option>
5642 <option value="sequencing_method">sequencing method used</option>
5643 </param>
5644 <when value="secondary_sample_accession">
5645 <param name="operation" type="select" label="Operator">
5646 <option value="equal">equal</option>
5647 <option value="different">different</option>
5648 </param>
5649 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5650 </when>
5651 <when value="environment_material">
5652 <param name="operation" type="select" label="Operator">
5653 <option value="equal">equal</option>
5654 <option value="different">different</option>
5655 </param>
5656 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5657 </when>
5658 <when value="dev_stage">
5659 <param name="operation" type="select" label="Operator">
5660 <option value="equal">equal</option>
5661 <option value="different">different</option>
5662 </param>
5663 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5664 </when>
5665 <when value="event_label">
5666 <param name="operation" type="select" label="Operator">
5667 <option value="equal">equal</option>
5668 <option value="different">different</option>
5669 </param>
5670 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5671 </when>
5672 <when value="center_name">
5673 <param name="operation" type="select" label="Operator">
5674 <option value="equal">equal</option>
5675 <option value="different">different</option>
5676 </param>
5677 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5678 </when>
5679 <when value="accession">
5680 <param name="operation" type="select" label="Operator">
5681 <option value="equal">equal</option>
5682 <option value="different">different</option>
5683 </param>
5684 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5685 </when>
5686 <when value="host_phenotype">
5687 <param name="operation" type="select" label="Operator">
5688 <option value="equal">equal</option>
5689 <option value="different">different</option>
5690 </param>
5691 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5692 </when>
5693 <when value="cell_line">
5694 <param name="operation" type="select" label="Operator">
5695 <option value="equal">equal</option>
5696 <option value="different">different</option>
5697 </param>
5698 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5699 </when>
5700 <when value="bio_material">
5701 <param name="operation" type="select" label="Operator">
5702 <option value="equal">equal</option>
5703 <option value="different">different</option>
5704 </param>
5705 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5706 </when>
5707 <when value="target_gene">
5708 <param name="operation" type="select" label="Operator">
5709 <option value="equal">equal</option>
5710 <option value="different">different</option>
5711 </param>
5712 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5713 </when>
5714 <when value="experimental_factor">
5715 <param name="operation" type="select" label="Operator">
5716 <option value="equal">equal</option>
5717 <option value="different">different</option>
5718 </param>
5719 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5720 </when>
5721 <when value="identified_by">
5722 <param name="operation" type="select" label="Operator">
5723 <option value="equal">equal</option>
5724 <option value="different">different</option>
5725 </param>
5726 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5727 </when>
5728 <when value="temperature">
5729 <param name="operation" type="select" label="Operator">
5730 <option value="equal">equal</option>
5731 <option value="different">different</option>
5732 <option value="lower">lower</option>
5733 <option value="equal or lower">equal or lower</option>
5734 <option value="higher">higher</option>
5735 <option value="equal or higher">equal or higher</option>
5736 </param>
5737 <param name="value" type="float" value="" label="Any integer"/>
5738 </when>
5739 <when value="sampling_platform">
5740 <param name="operation" type="select" label="Operator">
5741 <option value="equal">equal</option>
5742 <option value="different">different</option>
5743 </param>
5744 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5745 </when>
5746 <when value="collected_by">
5747 <param name="operation" type="select" label="Operator">
5748 <option value="equal">equal</option>
5749 <option value="different">different</option>
5750 </param>
5751 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5752 </when>
5753 <when value="collection_date">
5754 <param name="operation" type="select" label="Operator">
5755 <option value="equal">equal</option>
5756 <option value="different">different</option>
5757 <option value="lower">lower</option>
5758 <option value="equal or lower">equal or lower</option>
5759 <option value="higher">higher</option>
5760 <option value="equal or higher">equal or higher</option>
5761 </param>
5762 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
5763 </when>
5764 <when value="altitude">
5765 <param name="operation" type="select" label="Operator">
5766 <option value="equal">equal</option>
5767 <option value="different">different</option>
5768 <option value="lower">lower</option>
5769 <option value="equal or lower">equal or lower</option>
5770 <option value="higher">higher</option>
5771 <option value="equal or higher">equal or higher</option>
5772 </param>
5773 <param name="value" type="float" value="" label="Any integer"/>
5774 </when>
5775 <when value="host_sex">
5776 <param name="operation" type="select" label="Operator">
5777 <option value="equal">equal</option>
5778 <option value="different">different</option>
5779 </param>
5780 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5781 </when>
5782 <when value="investigation_type">
5783 <param name="operation" type="select" label="Operator">
5784 <option value="equal">equal</option>
5785 <option value="different">different</option>
5786 </param>
5787 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5788 </when>
5789 <when value="location">
5790 <conditional name="op">
5791 <param name="operation" type="select" label="Operation">
5792 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
5793 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
5794 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
5795 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
5796 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
5797 <option value="geo_point">An exact lat/lon position</option>
5798 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
5799 </param>
5800 <when value="geo_box2">
5801 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
5802 </when>
5803 <when value="geo_box1">
5804 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
5805 </when>
5806 <when value="geo_circ">
5807 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
5808 </when>
5809 <when value="geo_lat">
5810 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
5811 </when>
5812 <when value="geo_south">
5813 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
5814 </when>
5815 <when value="geo_point">
5816 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
5817 </when>
5818 <when value="geo_north">
5819 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
5820 </when>
5821 </conditional>
5822 </when>
5823 <when value="host_genotype">
5824 <param name="operation" type="select" label="Operator">
5825 <option value="equal">equal</option>
5826 <option value="different">different</option>
5827 </param>
5828 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5829 </when>
5830 <when value="ph">
5831 <param name="operation" type="select" label="Operator">
5832 <option value="equal">equal</option>
5833 <option value="different">different</option>
5834 <option value="lower">lower</option>
5835 <option value="equal or lower">equal or lower</option>
5836 <option value="higher">higher</option>
5837 <option value="equal or higher">equal or higher</option>
5838 </param>
5839 <param name="value" type="float" value="" label="Any integer"/>
5840 </when>
5841 <when value="broker_name">
5842 <param name="operation" type="select" label="Operator">
5843 <option value="equal">equal</option>
5844 <option value="different">different</option>
5845 </param>
5846 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5847 </when>
5848 <when value="project_name">
5849 <param name="operation" type="select" label="Operator">
5850 <option value="equal">equal</option>
5851 <option value="different">different</option>
5852 </param>
5853 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5854 </when>
5855 <when value="elevation">
5856 <param name="operation" type="select" label="Operator">
5857 <option value="equal">equal</option>
5858 <option value="different">different</option>
5859 <option value="lower">lower</option>
5860 <option value="equal or lower">equal or lower</option>
5861 <option value="higher">higher</option>
5862 <option value="equal or higher">equal or higher</option>
5863 </param>
5864 <param name="value" type="float" value="" label="Any integer"/>
5865 </when>
5866 <when value="description">
5867 <param name="operation" type="select" label="Operator">
5868 <option value="equal">equal</option>
5869 <option value="different">different</option>
5870 </param>
5871 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5872 </when>
5873 <when value="sample_alias">
5874 <param name="operation" type="select" label="Operator">
5875 <option value="equal">equal</option>
5876 <option value="different">different</option>
5877 </param>
5878 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5879 </when>
5880 <when value="checklist">
5881 <param name="operation" type="select" label="Operator">
5882 <option value="equal">equal</option>
5883 <option value="different">different</option>
5884 </param>
5885 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5886 </when>
5887 <when value="sampling_campaign">
5888 <param name="operation" type="select" label="Operator">
5889 <option value="equal">equal</option>
5890 <option value="different">different</option>
5891 </param>
5892 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5893 </when>
5894 <when value="protocol_label">
5895 <param name="operation" type="select" label="Operator">
5896 <option value="equal">equal</option>
5897 <option value="different">different</option>
5898 </param>
5899 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5900 </when>
5901 <when value="isolation_source">
5902 <param name="operation" type="select" label="Operator">
5903 <option value="equal">equal</option>
5904 <option value="different">different</option>
5905 </param>
5906 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5907 </when>
5908 <when value="sampling_site">
5909 <param name="operation" type="select" label="Operator">
5910 <option value="equal">equal</option>
5911 <option value="different">different</option>
5912 </param>
5913 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5914 </when>
5915 <when value="host_tax_id">
5916 <param name="operation" type="select" label="Operator">
5917 <option value="equal">equal</option>
5918 <option value="different">different</option>
5919 <option value="lower">lower</option>
5920 <option value="equal or lower">equal or lower</option>
5921 <option value="higher">higher</option>
5922 <option value="equal or higher">equal or higher</option>
5923 </param>
5924 <param name="value" type="float" value="" label="Any integer"/>
5925 </when>
5926 <when value="cultivar">
5927 <param name="operation" type="select" label="Operator">
5928 <option value="equal">equal</option>
5929 <option value="different">different</option>
5930 </param>
5931 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5932 </when>
5933 <when value="environment_biome">
5934 <param name="operation" type="select" label="Operator">
5935 <option value="equal">equal</option>
5936 <option value="different">different</option>
5937 </param>
5938 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5939 </when>
5940 <when value="environmental_package">
5941 <param name="operation" type="select" label="Operator">
5942 <option value="equal">equal</option>
5943 <option value="different">different</option>
5944 </param>
5945 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
5946 </when>
5947 <when value="marine_region">
5948 <param name="operation" type="select" label="Operator">
5949 <option value="equal">equal</option>
5950 <option value="different">different</option>
5951 </param>
5952 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5953 </when>
5954 <when value="first_public">
5955 <param name="operation" type="select" label="Operator">
5956 <option value="equal">equal</option>
5957 <option value="different">different</option>
5958 <option value="lower">lower</option>
5959 <option value="equal or lower">equal or lower</option>
5960 <option value="higher">higher</option>
5961 <option value="equal or higher">equal or higher</option>
5962 </param>
5963 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
5964 </when>
5965 <when value="environment_feature">
5966 <param name="operation" type="select" label="Operator">
5967 <option value="equal">equal</option>
5968 <option value="different">different</option>
5969 </param>
5970 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5971 </when>
5972 <when value="country">
5973 <param name="operation" type="select" label="Operator">
5974 <option value="equal">equal</option>
5975 <option value="different">different</option>
5976 </param>
5977 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5978 </when>
5979 <when value="host">
5980 <param name="operation" type="select" label="Operator">
5981 <option value="equal">equal</option>
5982 <option value="different">different</option>
5983 </param>
5984 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
5985 </when>
5986 <when value="salinity">
5987 <param name="operation" type="select" label="Operator">
5988 <option value="equal">equal</option>
5989 <option value="different">different</option>
5990 <option value="lower">lower</option>
5991 <option value="equal or lower">equal or lower</option>
5992 <option value="higher">higher</option>
5993 <option value="equal or higher">equal or higher</option>
5994 </param>
5995 <param name="value" type="float" value="" label="Any integer"/>
5996 </when>
5997 <when value="host_status">
5998 <param name="operation" type="select" label="Operator">
5999 <option value="equal">equal</option>
6000 <option value="different">different</option>
6001 </param>
6002 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6003 </when>
6004 <when value="strain">
6005 <param name="operation" type="select" label="Operator">
6006 <option value="equal">equal</option>
6007 <option value="different">different</option>
6008 </param>
6009 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6010 </when>
6011 <when value="depth">
6012 <param name="operation" type="select" label="Operator">
6013 <option value="equal">equal</option>
6014 <option value="different">different</option>
6015 <option value="lower">lower</option>
6016 <option value="equal or lower">equal or lower</option>
6017 <option value="higher">higher</option>
6018 <option value="equal or higher">equal or higher</option>
6019 </param>
6020 <param name="value" type="float" value="" label="Any integer"/>
6021 </when>
6022 <when value="tissue_type">
6023 <param name="operation" type="select" label="Operator">
6024 <option value="equal">equal</option>
6025 <option value="different">different</option>
6026 </param>
6027 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6028 </when>
6029 <when value="host_body_site">
6030 <param name="operation" type="select" label="Operator">
6031 <option value="equal">equal</option>
6032 <option value="different">different</option>
6033 </param>
6034 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6035 </when>
6036 <when value="host_growth_conditions">
6037 <param name="operation" type="select" label="Operator">
6038 <option value="equal">equal</option>
6039 <option value="different">different</option>
6040 </param>
6041 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6042 </when>
6043 <when value="sample_collection">
6044 <param name="operation" type="select" label="Operator">
6045 <option value="equal">equal</option>
6046 <option value="different">different</option>
6047 </param>
6048 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6049 </when>
6050 <when value="sequencing_method">
6051 <param name="operation" type="select" label="Operator">
6052 <option value="equal">equal</option>
6053 <option value="different">different</option>
6054 </param>
6055 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6056 </when>
6057 </conditional>
6058 </repeat>
6059 <conditional name="display_opt">
6060 <param argument="--display" type="select" label="Display option to specify the display format">
6061 <expand macro="display_options"/>
6062 </param>
6063 <when value="xml">
6064 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6065 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6066 </when>
6067 <when value="text">
6068 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6069 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6070 </when>
6071 <when value="fastq"/>
6072 <when value="html">
6073 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6074 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6075 </when>
6076 <when value="report">
6077 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6078 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6079 <param argument="--fields" type="select" multiple="true" label="Fields to return">
6080 <option value="accession">accession</option>
6081 <option value="secondary_sample_accession">secondary_sample_accession</option>
6082 <option value="bio_material">bio_material</option>
6083 <option value="cell_line">cell_line</option>
6084 <option value="collected_by">collected_by</option>
6085 <option value="collection_date">collection_date</option>
6086 <option value="country">country</option>
6087 <option value="marine_region">marine_region</option>
6088 <option value="cultivar">cultivar</option>
6089 <option value="description">description</option>
6090 <option value="dev_stage">dev_stage</option>
6091 <option value="first_public">first_public</option>
6092 <option value="identified_by">identified_by</option>
6093 <option value="isolation_source">isolation_source</option>
6094 <option value="location">location</option>
6095 <option value="strain">strain</option>
6096 <option value="tissue_type">tissue_type</option>
6097 <option value="tax_id">tax_id</option>
6098 <option value="scientific_name">scientific_name</option>
6099 <option value="sample_alias">sample_alias</option>
6100 <option value="checklist">checklist</option>
6101 <option value="center_name">center_name</option>
6102 <option value="depth">depth</option>
6103 <option value="elevation">elevation</option>
6104 <option value="altitude">altitude</option>
6105 <option value="environment_biome">environment_biome</option>
6106 <option value="environment_feature">environment_feature</option>
6107 <option value="environment_material">environment_material</option>
6108 <option value="temperature">temperature</option>
6109 <option value="salinity">salinity</option>
6110 <option value="sampling_campaign">sampling_campaign</option>
6111 <option value="sampling_site">sampling_site</option>
6112 <option value="sampling_platform">sampling_platform</option>
6113 <option value="protocol_label">protocol_label</option>
6114 <option value="project_name">project_name</option>
6115 <option value="host">host</option>
6116 <option value="host_tax_id">host_tax_id</option>
6117 <option value="host_status">host_status</option>
6118 <option value="host_sex">host_sex</option>
6119 <option value="submitted_host_sex">submitted_host_sex</option>
6120 <option value="host_body_site">host_body_site</option>
6121 <option value="host_gravidity">host_gravidity</option>
6122 <option value="host_phenotype">host_phenotype</option>
6123 <option value="host_genotype">host_genotype</option>
6124 <option value="host_growth_conditions">host_growth_conditions</option>
6125 <option value="environmental_package">environmental_package</option>
6126 <option value="investigation_type">investigation_type</option>
6127 <option value="experimental_factor">experimental_factor</option>
6128 <option value="sample_collection">sample_collection</option>
6129 <option value="sequencing_method">sequencing_method</option>
6130 <option value="target_gene">target_gene</option>
6131 <option value="ph">ph</option>
6132 <option value="broker_name">broker_name</option>
6133 <option value="event_label">event_label</option>
6134 </param>
6135 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
6136 <option value="secondary_sample_accession">secondary sample accession number</option>
6137 <option value="environment_material">Environment (Material)</option>
6138 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
6139 <option value="event_label">label given to sampling event</option>
6140 <option value="center_name">Submitting center</option>
6141 <option value="accession">accession number</option>
6142 <option value="host_phenotype">phenotype of host</option>
6143 <option value="cell_line">cell line from which the sample was obtained</option>
6144 <option value="bio_material">identifier for biological material including institute and collection code</option>
6145 <option value="target_gene">targeted gene or locus name for marker gene studies</option>
6146 <option value="experimental_factor">variable aspects of the experimental design</option>
6147 <option value="identified_by">name of the taxonomist who identified the specimen</option>
6148 <option value="temperature">Temperature (C)</option>
6149 <option value="sampling_platform">the large infrastructure from which this sample was collected</option>
6150 <option value="collected_by">name of the person who collected the specimen</option>
6151 <option value="collection_date">date that the specimen was collected</option>
6152 <option value="altitude">Altitude (m)</option>
6153 <option value="host_sex">physical sex of the host</option>
6154 <option value="investigation_type">the study type targeted by the sequencing</option>
6155 <option value="location">geographic location of isolation of the sample</option>
6156 <option value="host_genotype">genotype of host</option>
6157 <option value="ph">pH</option>
6158 <option value="broker_name">broker name</option>
6159 <option value="project_name">name of the project within which the sequencing was organized</option>
6160 <option value="elevation">Elevation (m)</option>
6161 <option value="description">brief sequence description</option>
6162 <option value="sample_alias">submitter's name for the sample</option>
6163 <option value="checklist">checklist name (or ID)</option>
6164 <option value="sampling_campaign">the activity within which this sample was collected</option>
6165 <option value="protocol_label">the protocol used to produce the sample</option>
6166 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
6167 <option value="sampling_site">the site/station where this sample was collection</option>
6168 <option value="host_tax_id">NCBI taxon id of the host</option>
6169 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
6170 <option value="environment_biome">Environment (Biome)</option>
6171 <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option>
6172 <option value="marine_region">geographical origin of the sample as defined by the marine region</option>
6173 <option value="first_public">date when made public</option>
6174 <option value="environment_feature">Environment (Feature)</option>
6175 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
6176 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
6177 <option value="salinity">Salinity (PSU)</option>
6178 <option value="host_status">condition of host (eg. diseased or healthy)</option>
6179 <option value="strain">strain from which sample was obtained</option>
6180 <option value="depth">Depth (m)</option>
6181 <option value="tissue_type">tissue type from which the sample was obtained</option>
6182 <option value="host_body_site">name of body site from where the sample was obtained</option>
6183 <option value="host_growth_conditions">literature reference giving growth conditions of the host</option>
6184 <option value="sample_collection">the method or deviced employed for collecting the sample</option>
6185 <option value="sequencing_method">sequencing method used</option>
6186 </param>
6187 </when>
6188 <when value="fasta"/>
6189 </conditional>
6190 </when>
6191 <when value="read_run">
6192 <repeat name="queries" title="Add a query">
6193 <param name="combination_operation" type="select" label="Combination operation">
6194 <option value="AND">AND</option>
6195 <option value="OR">OR</option>
6196 <option value="NOT">NOT</option>
6197 </param>
6198 <conditional name="filter_field">
6199 <param name="field" type="select" label="Field to query">
6200 <option value="secondary_sample_accession">secondary sample accession number</option>
6201 <option value="library_name">sequencing library name</option>
6202 <option value="read_count">number of reads</option>
6203 <option value="last_updated">date when last updated</option>
6204 <option value="center_name">Submitting center</option>
6205 <option value="submission_accession">submission accession number</option>
6206 <option value="nominal_length">average fragmentation size of paired reads</option>
6207 <option value="base_count">number of base pairs</option>
6208 <option value="run_accession">run accession number</option>
6209 <option value="library_selection">method used to select or enrich the material being sequenced</option>
6210 <option value="library_strategy">sequencing technique intended for the library</option>
6211 <option value="experiment_accession">experiment accession number</option>
6212 <option value="study_alias">submitter's name for the study</option>
6213 <option value="submitted_format"></option>
6214 <option value="broker_name">broker name</option>
6215 <option value="sample_alias">submitter's name for the sample</option>
6216 <option value="run_alias">submitter's name for the run</option>
6217 <option value="secondary_study_accession">project accession number</option>
6218 <option value="study_accession">study accession number</option>
6219 <option value="library_layout">sequencing library layout</option>
6220 <option value="library_source">source material being sequenced</option>
6221 <option value="experiment_title">brief experiment title</option>
6222 <option value="first_public">date when made public</option>
6223 <option value="instrument_platform">instrument platform used in sequencing experiment</option>
6224 <option value="instrument_model">instrument model used in sequencing experiment</option>
6225 <option value="sample_accession">sample accession number</option>
6226 <option value="experiment_alias">submitter's name for the experiment</option>
6227 <option value="study_title">brief sequencing study description</option>
6228 </param>
6229 <when value="secondary_sample_accession">
6230 <param name="operation" type="select" label="Operator">
6231 <option value="equal">equal</option>
6232 <option value="different">different</option>
6233 </param>
6234 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6235 </when>
6236 <when value="library_name">
6237 <param name="operation" type="select" label="Operator">
6238 <option value="equal">equal</option>
6239 <option value="different">different</option>
6240 </param>
6241 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6242 </when>
6243 <when value="read_count">
6244 <param name="operation" type="select" label="Operator">
6245 <option value="equal">equal</option>
6246 <option value="different">different</option>
6247 <option value="lower">lower</option>
6248 <option value="equal or lower">equal or lower</option>
6249 <option value="higher">higher</option>
6250 <option value="equal or higher">equal or higher</option>
6251 </param>
6252 <param name="value" type="float" value="" label="Any integer"/>
6253 </when>
6254 <when value="last_updated">
6255 <param name="operation" type="select" label="Operator">
6256 <option value="equal">equal</option>
6257 <option value="different">different</option>
6258 <option value="lower">lower</option>
6259 <option value="equal or lower">equal or lower</option>
6260 <option value="higher">higher</option>
6261 <option value="equal or higher">equal or higher</option>
6262 </param>
6263 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
6264 </when>
6265 <when value="center_name">
6266 <param name="operation" type="select" label="Operator">
6267 <option value="equal">equal</option>
6268 <option value="different">different</option>
6269 </param>
6270 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6271 </when>
6272 <when value="submission_accession">
6273 <param name="operation" type="select" label="Operator">
6274 <option value="equal">equal</option>
6275 <option value="different">different</option>
6276 </param>
6277 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6278 </when>
6279 <when value="nominal_length">
6280 <param name="operation" type="select" label="Operator">
6281 <option value="equal">equal</option>
6282 <option value="different">different</option>
6283 <option value="lower">lower</option>
6284 <option value="equal or lower">equal or lower</option>
6285 <option value="higher">higher</option>
6286 <option value="equal or higher">equal or higher</option>
6287 </param>
6288 <param name="value" type="float" value="" label="Any integer"/>
6289 </when>
6290 <when value="base_count">
6291 <param name="operation" type="select" label="Operator">
6292 <option value="equal">equal</option>
6293 <option value="different">different</option>
6294 <option value="lower">lower</option>
6295 <option value="equal or lower">equal or lower</option>
6296 <option value="higher">higher</option>
6297 <option value="equal or higher">equal or higher</option>
6298 </param>
6299 <param name="value" type="float" value="" label="Any integer"/>
6300 </when>
6301 <when value="run_accession">
6302 <param name="operation" type="select" label="Operator">
6303 <option value="equal">equal</option>
6304 <option value="different">different</option>
6305 </param>
6306 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6307 </when>
6308 <when value="library_selection">
6309 <param name="operation" type="select" label="Operator">
6310 <option value="equal">equal</option>
6311 <option value="different">different</option>
6312 </param>
6313 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6314 </when>
6315 <when value="library_strategy">
6316 <param name="operation" type="select" label="Operator">
6317 <option value="equal">equal</option>
6318 <option value="different">different</option>
6319 </param>
6320 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6321 </when>
6322 <when value="experiment_accession">
6323 <param name="operation" type="select" label="Operator">
6324 <option value="equal">equal</option>
6325 <option value="different">different</option>
6326 </param>
6327 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6328 </when>
6329 <when value="study_alias">
6330 <param name="operation" type="select" label="Operator">
6331 <option value="equal">equal</option>
6332 <option value="different">different</option>
6333 </param>
6334 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6335 </when>
6336 <when value="submitted_format">
6337 <param name="operation" type="select" label="Operator">
6338 <option value="equal">equal</option>
6339 <option value="different">different</option>
6340 </param>
6341 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6342 </when>
6343 <when value="broker_name">
6344 <param name="operation" type="select" label="Operator">
6345 <option value="equal">equal</option>
6346 <option value="different">different</option>
6347 </param>
6348 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6349 </when>
6350 <when value="sample_alias">
6351 <param name="operation" type="select" label="Operator">
6352 <option value="equal">equal</option>
6353 <option value="different">different</option>
6354 </param>
6355 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6356 </when>
6357 <when value="run_alias">
6358 <param name="operation" type="select" label="Operator">
6359 <option value="equal">equal</option>
6360 <option value="different">different</option>
6361 </param>
6362 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6363 </when>
6364 <when value="secondary_study_accession">
6365 <param name="operation" type="select" label="Operator">
6366 <option value="equal">equal</option>
6367 <option value="different">different</option>
6368 </param>
6369 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6370 </when>
6371 <when value="study_accession">
6372 <param name="operation" type="select" label="Operator">
6373 <option value="equal">equal</option>
6374 <option value="different">different</option>
6375 </param>
6376 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6377 </when>
6378 <when value="library_layout">
6379 <param name="operation" type="select" label="Operator">
6380 <option value="equal">equal</option>
6381 <option value="different">different</option>
6382 </param>
6383 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6384 </when>
6385 <when value="library_source">
6386 <param name="operation" type="select" label="Operator">
6387 <option value="equal">equal</option>
6388 <option value="different">different</option>
6389 </param>
6390 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6391 </when>
6392 <when value="experiment_title">
6393 <param name="operation" type="select" label="Operator">
6394 <option value="equal">equal</option>
6395 <option value="different">different</option>
6396 </param>
6397 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6398 </when>
6399 <when value="first_public">
6400 <param name="operation" type="select" label="Operator">
6401 <option value="equal">equal</option>
6402 <option value="different">different</option>
6403 <option value="lower">lower</option>
6404 <option value="equal or lower">equal or lower</option>
6405 <option value="higher">higher</option>
6406 <option value="equal or higher">equal or higher</option>
6407 </param>
6408 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
6409 </when>
6410 <when value="instrument_platform">
6411 <param name="operation" type="select" label="Operator">
6412 <option value="equal">equal</option>
6413 <option value="different">different</option>
6414 </param>
6415 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6416 </when>
6417 <when value="instrument_model">
6418 <param name="operation" type="select" label="Operator">
6419 <option value="equal">equal</option>
6420 <option value="different">different</option>
6421 </param>
6422 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6423 </when>
6424 <when value="sample_accession">
6425 <param name="operation" type="select" label="Operator">
6426 <option value="equal">equal</option>
6427 <option value="different">different</option>
6428 </param>
6429 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6430 </when>
6431 <when value="experiment_alias">
6432 <param name="operation" type="select" label="Operator">
6433 <option value="equal">equal</option>
6434 <option value="different">different</option>
6435 </param>
6436 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6437 </when>
6438 <when value="study_title">
6439 <param name="operation" type="select" label="Operator">
6440 <option value="equal">equal</option>
6441 <option value="different">different</option>
6442 </param>
6443 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6444 </when>
6445 </conditional>
6446 </repeat>
6447 <conditional name="display_opt">
6448 <param argument="--display" type="select" label="Display option to specify the display format">
6449 <expand macro="display_options"/>
6450 </param>
6451 <when value="xml">
6452 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6453 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6454 </when>
6455 <when value="text">
6456 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6457 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6458 </when>
6459 <when value="fastq"/>
6460 <when value="html">
6461 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6462 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6463 </when>
6464 <when value="report">
6465 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6466 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6467 <param argument="--fields" type="select" multiple="true" label="Fields to return">
6468 <option value="study_accession">study_accession</option>
6469 <option value="secondary_study_accession">secondary_study_accession</option>
6470 <option value="sample_accession">sample_accession</option>
6471 <option value="secondary_sample_accession">secondary_sample_accession</option>
6472 <option value="experiment_accession">experiment_accession</option>
6473 <option value="run_accession">run_accession</option>
6474 <option value="submission_accession">submission_accession</option>
6475 <option value="tax_id">tax_id</option>
6476 <option value="scientific_name">scientific_name</option>
6477 <option value="instrument_platform">instrument_platform</option>
6478 <option value="instrument_model">instrument_model</option>
6479 <option value="library_name">library_name</option>
6480 <option value="nominal_length">nominal_length</option>
6481 <option value="library_layout">library_layout</option>
6482 <option value="library_strategy">library_strategy</option>
6483 <option value="library_source">library_source</option>
6484 <option value="library_selection">library_selection</option>
6485 <option value="read_count">read_count</option>
6486 <option value="base_count">base_count</option>
6487 <option value="center_name">center_name</option>
6488 <option value="first_public">first_public</option>
6489 <option value="last_updated">last_updated</option>
6490 <option value="experiment_title">experiment_title</option>
6491 <option value="study_title">study_title</option>
6492 <option value="study_alias">study_alias</option>
6493 <option value="experiment_alias">experiment_alias</option>
6494 <option value="run_alias">run_alias</option>
6495 <option value="fastq_bytes">fastq_bytes</option>
6496 <option value="fastq_md5">fastq_md5</option>
6497 <option value="fastq_ftp">fastq_ftp</option>
6498 <option value="fastq_aspera">fastq_aspera</option>
6499 <option value="fastq_galaxy">fastq_galaxy</option>
6500 <option value="submitted_bytes">submitted_bytes</option>
6501 <option value="submitted_md5">submitted_md5</option>
6502 <option value="submitted_ftp">submitted_ftp</option>
6503 <option value="submitted_aspera">submitted_aspera</option>
6504 <option value="submitted_galaxy">submitted_galaxy</option>
6505 <option value="submitted_format">submitted_format</option>
6506 <option value="sra_bytes">sra_bytes</option>
6507 <option value="sra_md5">sra_md5</option>
6508 <option value="sra_ftp">sra_ftp</option>
6509 <option value="sra_aspera">sra_aspera</option>
6510 <option value="sra_galaxy">sra_galaxy</option>
6511 <option value="cram_index_ftp">cram_index_ftp</option>
6512 <option value="cram_index_aspera">cram_index_aspera</option>
6513 <option value="cram_index_galaxy">cram_index_galaxy</option>
6514 <option value="sample_alias">sample_alias</option>
6515 <option value="broker_name">broker_name</option>
6516 </param>
6517 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
6518 <option value="secondary_sample_accession">secondary sample accession number</option>
6519 <option value="library_name">sequencing library name</option>
6520 <option value="read_count">number of reads</option>
6521 <option value="last_updated">date when last updated</option>
6522 <option value="center_name">Submitting center</option>
6523 <option value="submission_accession">submission accession number</option>
6524 <option value="nominal_length">average fragmentation size of paired reads</option>
6525 <option value="base_count">number of base pairs</option>
6526 <option value="run_accession">run accession number</option>
6527 <option value="library_selection">method used to select or enrich the material being sequenced</option>
6528 <option value="library_strategy">sequencing technique intended for the library</option>
6529 <option value="experiment_accession">experiment accession number</option>
6530 <option value="study_alias">submitter's name for the study</option>
6531 <option value="submitted_format"></option>
6532 <option value="broker_name">broker name</option>
6533 <option value="sample_alias">submitter's name for the sample</option>
6534 <option value="run_alias">submitter's name for the run</option>
6535 <option value="secondary_study_accession">project accession number</option>
6536 <option value="study_accession">study accession number</option>
6537 <option value="library_layout">sequencing library layout</option>
6538 <option value="library_source">source material being sequenced</option>
6539 <option value="experiment_title">brief experiment title</option>
6540 <option value="first_public">date when made public</option>
6541 <option value="instrument_platform">instrument platform used in sequencing experiment</option>
6542 <option value="instrument_model">instrument model used in sequencing experiment</option>
6543 <option value="sample_accession">sample accession number</option>
6544 <option value="experiment_alias">submitter's name for the experiment</option>
6545 <option value="study_title">brief sequencing study description</option>
6546 </param>
6547 </when>
6548 <when value="fasta"/>
6549 </conditional>
6550 </when>
6551 <when value="read_study">
6552 <repeat name="queries" title="Add a query">
6553 <param name="combination_operation" type="select" label="Combination operation">
6554 <option value="AND">AND</option>
6555 <option value="OR">OR</option>
6556 <option value="NOT">NOT</option>
6557 </param>
6558 <conditional name="filter_field">
6559 <param name="field" type="select" label="Field to query">
6560 <option value="study_title">brief sequencing study description</option>
6561 <option value="secondary_study_accession">project accession number</option>
6562 <option value="study_alias">submitter's name for the study</option>
6563 <option value="study_accession">study accession number</option>
6564 </param>
6565 <when value="study_title">
6566 <param name="operation" type="select" label="Operator">
6567 <option value="equal">equal</option>
6568 <option value="different">different</option>
6569 </param>
6570 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6571 </when>
6572 <when value="secondary_study_accession">
6573 <param name="operation" type="select" label="Operator">
6574 <option value="equal">equal</option>
6575 <option value="different">different</option>
6576 </param>
6577 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6578 </when>
6579 <when value="study_alias">
6580 <param name="operation" type="select" label="Operator">
6581 <option value="equal">equal</option>
6582 <option value="different">different</option>
6583 </param>
6584 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6585 </when>
6586 <when value="study_accession">
6587 <param name="operation" type="select" label="Operator">
6588 <option value="equal">equal</option>
6589 <option value="different">different</option>
6590 </param>
6591 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6592 </when>
6593 </conditional>
6594 </repeat>
6595 <conditional name="display_opt">
6596 <param argument="--display" type="select" label="Display option to specify the display format">
6597 <expand macro="display_options"/>
6598 </param>
6599 <when value="xml">
6600 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6601 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6602 </when>
6603 <when value="text">
6604 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6605 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6606 </when>
6607 <when value="fastq"/>
6608 <when value="html">
6609 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6610 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6611 </when>
6612 <when value="report">
6613 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6614 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6615 <param argument="--fields" type="select" multiple="true" label="Fields to return">
6616 <option value="study_accession">study_accession</option>
6617 <option value="secondary_study_accession">secondary_study_accession</option>
6618 <option value="study_title">study_title</option>
6619 <option value="study_alias">study_alias</option>
6620 </param>
6621 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
6622 <option value="study_title">brief sequencing study description</option>
6623 <option value="secondary_study_accession">project accession number</option>
6624 <option value="study_alias">submitter's name for the study</option>
6625 <option value="study_accession">study accession number</option>
6626 </param>
6627 </when>
6628 <when value="fasta"/>
6629 </conditional>
6630 </when>
6631 <when value="read_experiment">
6632 <repeat name="queries" title="Add a query">
6633 <param name="combination_operation" type="select" label="Combination operation">
6634 <option value="AND">AND</option>
6635 <option value="OR">OR</option>
6636 <option value="NOT">NOT</option>
6637 </param>
6638 <conditional name="filter_field">
6639 <param name="field" type="select" label="Field to query">
6640 <option value="library_name">sequencing library name</option>
6641 <option value="study_title">brief sequencing study description</option>
6642 <option value="instrument_platform">instrument platform used in sequencing experiment</option>
6643 <option value="instrument_model">instrument model used in sequencing experiment</option>
6644 <option value="study_alias">submitter's name for the study</option>
6645 <option value="experiment_alias">submitter's name for the experiment</option>
6646 <option value="secondary_study_accession">project accession number</option>
6647 <option value="study_accession">study accession number</option>
6648 <option value="library_selection">method used to select or enrich the material being sequenced</option>
6649 <option value="library_layout">sequencing library layout</option>
6650 <option value="library_strategy">sequencing technique intended for the library</option>
6651 <option value="experiment_accession">experiment accession number</option>
6652 <option value="library_source">source material being sequenced</option>
6653 <option value="experiment_title">brief experiment title</option>
6654 </param>
6655 <when value="library_name">
6656 <param name="operation" type="select" label="Operator">
6657 <option value="equal">equal</option>
6658 <option value="different">different</option>
6659 </param>
6660 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6661 </when>
6662 <when value="study_title">
6663 <param name="operation" type="select" label="Operator">
6664 <option value="equal">equal</option>
6665 <option value="different">different</option>
6666 </param>
6667 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6668 </when>
6669 <when value="instrument_platform">
6670 <param name="operation" type="select" label="Operator">
6671 <option value="equal">equal</option>
6672 <option value="different">different</option>
6673 </param>
6674 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6675 </when>
6676 <when value="instrument_model">
6677 <param name="operation" type="select" label="Operator">
6678 <option value="equal">equal</option>
6679 <option value="different">different</option>
6680 </param>
6681 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6682 </when>
6683 <when value="study_alias">
6684 <param name="operation" type="select" label="Operator">
6685 <option value="equal">equal</option>
6686 <option value="different">different</option>
6687 </param>
6688 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6689 </when>
6690 <when value="experiment_alias">
6691 <param name="operation" type="select" label="Operator">
6692 <option value="equal">equal</option>
6693 <option value="different">different</option>
6694 </param>
6695 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6696 </when>
6697 <when value="secondary_study_accession">
6698 <param name="operation" type="select" label="Operator">
6699 <option value="equal">equal</option>
6700 <option value="different">different</option>
6701 </param>
6702 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6703 </when>
6704 <when value="study_accession">
6705 <param name="operation" type="select" label="Operator">
6706 <option value="equal">equal</option>
6707 <option value="different">different</option>
6708 </param>
6709 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6710 </when>
6711 <when value="library_selection">
6712 <param name="operation" type="select" label="Operator">
6713 <option value="equal">equal</option>
6714 <option value="different">different</option>
6715 </param>
6716 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6717 </when>
6718 <when value="library_layout">
6719 <param name="operation" type="select" label="Operator">
6720 <option value="equal">equal</option>
6721 <option value="different">different</option>
6722 </param>
6723 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6724 </when>
6725 <when value="library_strategy">
6726 <param name="operation" type="select" label="Operator">
6727 <option value="equal">equal</option>
6728 <option value="different">different</option>
6729 </param>
6730 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6731 </when>
6732 <when value="experiment_accession">
6733 <param name="operation" type="select" label="Operator">
6734 <option value="equal">equal</option>
6735 <option value="different">different</option>
6736 </param>
6737 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6738 </when>
6739 <when value="library_source">
6740 <param name="operation" type="select" label="Operator">
6741 <option value="equal">equal</option>
6742 <option value="different">different</option>
6743 </param>
6744 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6745 </when>
6746 <when value="experiment_title">
6747 <param name="operation" type="select" label="Operator">
6748 <option value="equal">equal</option>
6749 <option value="different">different</option>
6750 </param>
6751 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6752 </when>
6753 </conditional>
6754 </repeat>
6755 <conditional name="display_opt">
6756 <param argument="--display" type="select" label="Display option to specify the display format">
6757 <expand macro="display_options"/>
6758 </param>
6759 <when value="xml">
6760 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6761 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6762 </when>
6763 <when value="text">
6764 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6765 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6766 </when>
6767 <when value="fastq"/>
6768 <when value="html">
6769 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6770 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6771 </when>
6772 <when value="report">
6773 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6774 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6775 <param argument="--fields" type="select" multiple="true" label="Fields to return">
6776 <option value="study_accession">study_accession</option>
6777 <option value="secondary_study_accession">secondary_study_accession</option>
6778 <option value="experiment_accession">experiment_accession</option>
6779 <option value="instrument_platform">instrument_platform</option>
6780 <option value="instrument_model">instrument_model</option>
6781 <option value="library_name">library_name</option>
6782 <option value="library_layout">library_layout</option>
6783 <option value="library_strategy">library_strategy</option>
6784 <option value="library_source">library_source</option>
6785 <option value="library_selection">library_selection</option>
6786 <option value="experiment_title">experiment_title</option>
6787 <option value="study_title">study_title</option>
6788 <option value="study_alias">study_alias</option>
6789 <option value="experiment_alias">experiment_alias</option>
6790 </param>
6791 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
6792 <option value="library_name">sequencing library name</option>
6793 <option value="study_title">brief sequencing study description</option>
6794 <option value="instrument_platform">instrument platform used in sequencing experiment</option>
6795 <option value="instrument_model">instrument model used in sequencing experiment</option>
6796 <option value="study_alias">submitter's name for the study</option>
6797 <option value="experiment_alias">submitter's name for the experiment</option>
6798 <option value="secondary_study_accession">project accession number</option>
6799 <option value="study_accession">study accession number</option>
6800 <option value="library_selection">method used to select or enrich the material being sequenced</option>
6801 <option value="library_layout">sequencing library layout</option>
6802 <option value="library_strategy">sequencing technique intended for the library</option>
6803 <option value="experiment_accession">experiment accession number</option>
6804 <option value="library_source">source material being sequenced</option>
6805 <option value="experiment_title">brief experiment title</option>
6806 </param>
6807 </when>
6808 <when value="fasta"/>
6809 </conditional>
6810 </when>
6811 <when value="analysis">
6812 <repeat name="queries" title="Add a query">
6813 <param name="combination_operation" type="select" label="Combination operation">
6814 <option value="AND">AND</option>
6815 <option value="OR">OR</option>
6816 <option value="NOT">NOT</option>
6817 </param>
6818 <conditional name="filter_field">
6819 <param name="field" type="select" label="Field to query">
6820 <option value="secondary_sample_accession">secondary sample accession number</option>
6821 <option value="broker_name">broker name</option>
6822 <option value="study_accession">study accession number</option>
6823 <option value="last_updated">date when last updated</option>
6824 <option value="first_public">date when made public</option>
6825 <option value="sample_alias">submitter's name for the sample</option>
6826 <option value="center_name">Submitting center</option>
6827 <option value="analysis_title">brief sequence analysis description</option>
6828 <option value="sample_accession">sample accession number</option>
6829 <option value="analysis_accession">analysis accession number</option>
6830 <option value="secondary_study_accession">project accession number</option>
6831 <option value="analysis_alias">submitter's name for the analysis</option>
6832 <option value="analysis_type">type of sequence analysis</option>
6833 <option value="study_title">brief sequencing study description</option>
6834 <option value="study_alias">submitter's name for the study</option>
6835 </param>
6836 <when value="secondary_sample_accession">
6837 <param name="operation" type="select" label="Operator">
6838 <option value="equal">equal</option>
6839 <option value="different">different</option>
6840 </param>
6841 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6842 </when>
6843 <when value="broker_name">
6844 <param name="operation" type="select" label="Operator">
6845 <option value="equal">equal</option>
6846 <option value="different">different</option>
6847 </param>
6848 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6849 </when>
6850 <when value="study_accession">
6851 <param name="operation" type="select" label="Operator">
6852 <option value="equal">equal</option>
6853 <option value="different">different</option>
6854 </param>
6855 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6856 </when>
6857 <when value="last_updated">
6858 <param name="operation" type="select" label="Operator">
6859 <option value="equal">equal</option>
6860 <option value="different">different</option>
6861 <option value="lower">lower</option>
6862 <option value="equal or lower">equal or lower</option>
6863 <option value="higher">higher</option>
6864 <option value="equal or higher">equal or higher</option>
6865 </param>
6866 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
6867 </when>
6868 <when value="first_public">
6869 <param name="operation" type="select" label="Operator">
6870 <option value="equal">equal</option>
6871 <option value="different">different</option>
6872 <option value="lower">lower</option>
6873 <option value="equal or lower">equal or lower</option>
6874 <option value="higher">higher</option>
6875 <option value="equal or higher">equal or higher</option>
6876 </param>
6877 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
6878 </when>
6879 <when value="sample_alias">
6880 <param name="operation" type="select" label="Operator">
6881 <option value="equal">equal</option>
6882 <option value="different">different</option>
6883 </param>
6884 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6885 </when>
6886 <when value="center_name">
6887 <param name="operation" type="select" label="Operator">
6888 <option value="equal">equal</option>
6889 <option value="different">different</option>
6890 </param>
6891 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6892 </when>
6893 <when value="analysis_title">
6894 <param name="operation" type="select" label="Operator">
6895 <option value="equal">equal</option>
6896 <option value="different">different</option>
6897 </param>
6898 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6899 </when>
6900 <when value="sample_accession">
6901 <param name="operation" type="select" label="Operator">
6902 <option value="equal">equal</option>
6903 <option value="different">different</option>
6904 </param>
6905 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6906 </when>
6907 <when value="analysis_accession">
6908 <param name="operation" type="select" label="Operator">
6909 <option value="equal">equal</option>
6910 <option value="different">different</option>
6911 </param>
6912 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6913 </when>
6914 <when value="secondary_study_accession">
6915 <param name="operation" type="select" label="Operator">
6916 <option value="equal">equal</option>
6917 <option value="different">different</option>
6918 </param>
6919 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6920 </when>
6921 <when value="analysis_alias">
6922 <param name="operation" type="select" label="Operator">
6923 <option value="equal">equal</option>
6924 <option value="different">different</option>
6925 </param>
6926 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6927 </when>
6928 <when value="analysis_type">
6929 <param name="operation" type="select" label="Operator">
6930 <option value="equal">equal</option>
6931 <option value="different">different</option>
6932 </param>
6933 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
6934 </when>
6935 <when value="study_title">
6936 <param name="operation" type="select" label="Operator">
6937 <option value="equal">equal</option>
6938 <option value="different">different</option>
6939 </param>
6940 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6941 </when>
6942 <when value="study_alias">
6943 <param name="operation" type="select" label="Operator">
6944 <option value="equal">equal</option>
6945 <option value="different">different</option>
6946 </param>
6947 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
6948 </when>
6949 </conditional>
6950 </repeat>
6951 <conditional name="display_opt">
6952 <param argument="--display" type="select" label="Display option to specify the display format">
6953 <expand macro="display_options"/>
6954 </param>
6955 <when value="xml">
6956 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6957 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6958 </when>
6959 <when value="text">
6960 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6961 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6962 </when>
6963 <when value="fastq"/>
6964 <when value="html">
6965 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6966 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6967 </when>
6968 <when value="report">
6969 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
6970 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
6971 <param argument="--fields" type="select" multiple="true" label="Fields to return">
6972 <option value="analysis_accession">analysis_accession</option>
6973 <option value="study_accession">study_accession</option>
6974 <option value="secondary_study_accession">secondary_study_accession</option>
6975 <option value="sample_accession">sample_accession</option>
6976 <option value="secondary_sample_accession">secondary_sample_accession</option>
6977 <option value="analysis_title">analysis_title</option>
6978 <option value="analysis_type">analysis_type</option>
6979 <option value="center_name">center_name</option>
6980 <option value="first_public">first_public</option>
6981 <option value="last_updated">last_updated</option>
6982 <option value="study_title">study_title</option>
6983 <option value="tax_id">tax_id</option>
6984 <option value="scientific_name">scientific_name</option>
6985 <option value="analysis_alias">analysis_alias</option>
6986 <option value="study_alias">study_alias</option>
6987 <option value="submitted_bytes">submitted_bytes</option>
6988 <option value="submitted_md5">submitted_md5</option>
6989 <option value="submitted_ftp">submitted_ftp</option>
6990 <option value="submitted_aspera">submitted_aspera</option>
6991 <option value="submitted_galaxy">submitted_galaxy</option>
6992 <option value="sample_alias">sample_alias</option>
6993 <option value="broker_name">broker_name</option>
6994 </param>
6995 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
6996 <option value="secondary_sample_accession">secondary sample accession number</option>
6997 <option value="broker_name">broker name</option>
6998 <option value="study_accession">study accession number</option>
6999 <option value="last_updated">date when last updated</option>
7000 <option value="first_public">date when made public</option>
7001 <option value="sample_alias">submitter's name for the sample</option>
7002 <option value="center_name">Submitting center</option>
7003 <option value="analysis_title">brief sequence analysis description</option>
7004 <option value="sample_accession">sample accession number</option>
7005 <option value="analysis_accession">analysis accession number</option>
7006 <option value="secondary_study_accession">project accession number</option>
7007 <option value="analysis_alias">submitter's name for the analysis</option>
7008 <option value="analysis_type">type of sequence analysis</option>
7009 <option value="study_title">brief sequencing study description</option>
7010 <option value="study_alias">submitter's name for the study</option>
7011 </param>
7012 </when>
7013 <when value="fasta"/>
7014 </conditional>
7015 </when>
7016 <when value="sequence_update">
7017 <repeat name="queries" title="Add a query">
7018 <param name="combination_operation" type="select" label="Combination operation">
7019 <option value="AND">AND</option>
7020 <option value="OR">OR</option>
7021 <option value="NOT">NOT</option>
7022 </param>
7023 <conditional name="filter_field">
7024 <param name="field" type="select" label="Field to query">
7025 <option value="mol_type">in vivo molecule type of the sequence</option>
7026 <option value="last_updated">date when last updated</option>
7027 <option value="sequence_md5"></option>
7028 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
7029 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
7030 <option value="sex">sex of the organism from which the sample was obtained</option>
7031 <option value="keywords">keywords associated with sequence</option>
7032 <option value="collected_by">name of the person who collected the specimen</option>
7033 <option value="cell_line">cell line from which the sample was obtained</option>
7034 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
7035 <option value="bio_material">identifier for biological material including institute and collection code</option>
7036 <option value="identified_by">name of the taxonomist who identified the specimen</option>
7037 <option value="cell_type">cell type from which the sample was obtained</option>
7038 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
7039 <option value="tax_division">taxonomic division</option>
7040 <option value="collection_date">date that the specimen was collected</option>
7041 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
7042 <option value="altitude">Altitude (m)</option>
7043 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
7044 <option value="isolate">individual isolate from which sample was obtained</option>
7045 <option value="location">geographic location of isolation of the sample</option>
7046 <option value="study_accession">study accession number</option>
7047 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
7048 <option value="description">brief sequence description</option>
7049 <option value="accession">accession number</option>
7050 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
7051 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
7052 <option value="tissue_type">tissue type from which the sample was obtained</option>
7053 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
7054 <option value="tissue_lib">tissue library from which sample was obtained</option>
7055 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
7056 <option value="base_count">number of base pairs</option>
7057 <option value="topology">sequence topology: circular or linear</option>
7058 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
7059 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
7060 <option value="first_public">date when made public</option>
7061 <option value="strain">strain from which sample was obtained</option>
7062 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
7063 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
7064 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
7065 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
7066 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
7067 <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option>
7068 <option value="dataclass">sequence data class</option>
7069 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
7070 </param>
7071 <when value="mol_type">
7072 <param name="operation" type="select" label="Operator">
7073 <option value="equal">equal</option>
7074 <option value="different">different</option>
7075 </param>
7076 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7077 </when>
7078 <when value="last_updated">
7079 <param name="operation" type="select" label="Operator">
7080 <option value="equal">equal</option>
7081 <option value="different">different</option>
7082 <option value="lower">lower</option>
7083 <option value="equal or lower">equal or lower</option>
7084 <option value="higher">higher</option>
7085 <option value="equal or higher">equal or higher</option>
7086 </param>
7087 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
7088 </when>
7089 <when value="sequence_md5">
7090 <param name="operation" type="select" label="Operator">
7091 <option value="equal">equal</option>
7092 <option value="different">different</option>
7093 </param>
7094 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7095 </when>
7096 <when value="haplotype">
7097 <param name="operation" type="select" label="Operator">
7098 <option value="equal">equal</option>
7099 <option value="different">different</option>
7100 </param>
7101 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7102 </when>
7103 <when value="serotype">
7104 <param name="operation" type="select" label="Operator">
7105 <option value="equal">equal</option>
7106 <option value="different">different</option>
7107 </param>
7108 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7109 </when>
7110 <when value="sex">
7111 <param name="operation" type="select" label="Operator">
7112 <option value="equal">equal</option>
7113 <option value="different">different</option>
7114 </param>
7115 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7116 </when>
7117 <when value="keywords">
7118 <param name="operation" type="select" label="Operator">
7119 <option value="equal">equal</option>
7120 <option value="different">different</option>
7121 </param>
7122 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7123 </when>
7124 <when value="collected_by">
7125 <param name="operation" type="select" label="Operator">
7126 <option value="equal">equal</option>
7127 <option value="different">different</option>
7128 </param>
7129 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7130 </when>
7131 <when value="cell_line">
7132 <param name="operation" type="select" label="Operator">
7133 <option value="equal">equal</option>
7134 <option value="different">different</option>
7135 </param>
7136 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7137 </when>
7138 <when value="ecotype">
7139 <param name="operation" type="select" label="Operator">
7140 <option value="equal">equal</option>
7141 <option value="different">different</option>
7142 </param>
7143 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7144 </when>
7145 <when value="bio_material">
7146 <param name="operation" type="select" label="Operator">
7147 <option value="equal">equal</option>
7148 <option value="different">different</option>
7149 </param>
7150 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7151 </when>
7152 <when value="identified_by">
7153 <param name="operation" type="select" label="Operator">
7154 <option value="equal">equal</option>
7155 <option value="different">different</option>
7156 </param>
7157 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7158 </when>
7159 <when value="cell_type">
7160 <param name="operation" type="select" label="Operator">
7161 <option value="equal">equal</option>
7162 <option value="different">different</option>
7163 </param>
7164 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7165 </when>
7166 <when value="lab_host">
7167 <param name="operation" type="select" label="Operator">
7168 <option value="equal">equal</option>
7169 <option value="different">different</option>
7170 </param>
7171 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7172 </when>
7173 <when value="tax_division">
7174 <param name="operation" type="select" label="Operator">
7175 <option value="equal">equal</option>
7176 <option value="different">different</option>
7177 </param>
7178 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7179 </when>
7180 <when value="collection_date">
7181 <param name="operation" type="select" label="Operator">
7182 <option value="equal">equal</option>
7183 <option value="different">different</option>
7184 <option value="lower">lower</option>
7185 <option value="equal or lower">equal or lower</option>
7186 <option value="higher">higher</option>
7187 <option value="equal or higher">equal or higher</option>
7188 </param>
7189 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
7190 </when>
7191 <when value="specimen_voucher">
7192 <param name="operation" type="select" label="Operator">
7193 <option value="equal">equal</option>
7194 <option value="different">different</option>
7195 </param>
7196 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7197 </when>
7198 <when value="altitude">
7199 <param name="operation" type="select" label="Operator">
7200 <option value="equal">equal</option>
7201 <option value="different">different</option>
7202 <option value="lower">lower</option>
7203 <option value="equal or lower">equal or lower</option>
7204 <option value="higher">higher</option>
7205 <option value="equal or higher">equal or higher</option>
7206 </param>
7207 <param name="value" type="float" value="" label="Any integer"/>
7208 </when>
7209 <when value="dev_stage">
7210 <param name="operation" type="select" label="Operator">
7211 <option value="equal">equal</option>
7212 <option value="different">different</option>
7213 </param>
7214 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7215 </when>
7216 <when value="isolate">
7217 <param name="operation" type="select" label="Operator">
7218 <option value="equal">equal</option>
7219 <option value="different">different</option>
7220 </param>
7221 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7222 </when>
7223 <when value="location">
7224 <conditional name="op">
7225 <param name="operation" type="select" label="Operation">
7226 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
7227 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
7228 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
7229 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
7230 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
7231 <option value="geo_point">An exact lat/lon position</option>
7232 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
7233 </param>
7234 <when value="geo_box2">
7235 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
7236 </when>
7237 <when value="geo_box1">
7238 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
7239 </when>
7240 <when value="geo_circ">
7241 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
7242 </when>
7243 <when value="geo_lat">
7244 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
7245 </when>
7246 <when value="geo_south">
7247 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
7248 </when>
7249 <when value="geo_point">
7250 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
7251 </when>
7252 <when value="geo_north">
7253 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
7254 </when>
7255 </conditional>
7256 </when>
7257 <when value="study_accession">
7258 <param name="operation" type="select" label="Operator">
7259 <option value="equal">equal</option>
7260 <option value="different">different</option>
7261 </param>
7262 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7263 </when>
7264 <when value="germline">
7265 <param name="operation" type="select" label="Operator">
7266 <option value="equal">equal</option>
7267 </param>
7268 <param name="value" type="select" label="Value">
7269 <option value="yes">yes</option>
7270 <option value="true">true</option>
7271 <option value="no">no</option>
7272 <option value="false">false</option>
7273 </param>
7274 </when>
7275 <when value="description">
7276 <param name="operation" type="select" label="Operator">
7277 <option value="equal">equal</option>
7278 <option value="different">different</option>
7279 </param>
7280 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7281 </when>
7282 <when value="accession">
7283 <param name="operation" type="select" label="Operator">
7284 <option value="equal">equal</option>
7285 <option value="different">different</option>
7286 </param>
7287 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7288 </when>
7289 <when value="isolation_source">
7290 <param name="operation" type="select" label="Operator">
7291 <option value="equal">equal</option>
7292 <option value="different">different</option>
7293 </param>
7294 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7295 </when>
7296 <when value="mating_type">
7297 <param name="operation" type="select" label="Operator">
7298 <option value="equal">equal</option>
7299 <option value="different">different</option>
7300 </param>
7301 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7302 </when>
7303 <when value="tissue_type">
7304 <param name="operation" type="select" label="Operator">
7305 <option value="equal">equal</option>
7306 <option value="different">different</option>
7307 </param>
7308 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7309 </when>
7310 <when value="sub_strain">
7311 <param name="operation" type="select" label="Operator">
7312 <option value="equal">equal</option>
7313 <option value="different">different</option>
7314 </param>
7315 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7316 </when>
7317 <when value="tissue_lib">
7318 <param name="operation" type="select" label="Operator">
7319 <option value="equal">equal</option>
7320 <option value="different">different</option>
7321 </param>
7322 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7323 </when>
7324 <when value="cultivar">
7325 <param name="operation" type="select" label="Operator">
7326 <option value="equal">equal</option>
7327 <option value="different">different</option>
7328 </param>
7329 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7330 </when>
7331 <when value="base_count">
7332 <param name="operation" type="select" label="Operator">
7333 <option value="equal">equal</option>
7334 <option value="different">different</option>
7335 <option value="lower">lower</option>
7336 <option value="equal or lower">equal or lower</option>
7337 <option value="higher">higher</option>
7338 <option value="equal or higher">equal or higher</option>
7339 </param>
7340 <param name="value" type="float" value="" label="Any integer"/>
7341 </when>
7342 <when value="topology">
7343 <param name="operation" type="select" label="Operator">
7344 <option value="equal">equal</option>
7345 <option value="different">different</option>
7346 </param>
7347 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7348 </when>
7349 <when value="sub_species">
7350 <param name="operation" type="select" label="Operator">
7351 <option value="equal">equal</option>
7352 <option value="different">different</option>
7353 </param>
7354 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7355 </when>
7356 <when value="environmental_sample">
7357 <param name="operation" type="select" label="Operator">
7358 <option value="equal">equal</option>
7359 </param>
7360 <param name="value" type="select" label="Value">
7361 <option value="yes">yes</option>
7362 <option value="true">true</option>
7363 <option value="no">no</option>
7364 <option value="false">false</option>
7365 </param>
7366 </when>
7367 <when value="first_public">
7368 <param name="operation" type="select" label="Operator">
7369 <option value="equal">equal</option>
7370 <option value="different">different</option>
7371 <option value="lower">lower</option>
7372 <option value="equal or lower">equal or lower</option>
7373 <option value="higher">higher</option>
7374 <option value="equal or higher">equal or higher</option>
7375 </param>
7376 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
7377 </when>
7378 <when value="strain">
7379 <param name="operation" type="select" label="Operator">
7380 <option value="equal">equal</option>
7381 <option value="different">different</option>
7382 </param>
7383 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7384 </when>
7385 <when value="country">
7386 <param name="operation" type="select" label="Operator">
7387 <option value="equal">equal</option>
7388 <option value="different">different</option>
7389 </param>
7390 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7391 </when>
7392 <when value="variety">
7393 <param name="operation" type="select" label="Operator">
7394 <option value="equal">equal</option>
7395 <option value="different">different</option>
7396 </param>
7397 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7398 </when>
7399 <when value="host">
7400 <param name="operation" type="select" label="Operator">
7401 <option value="equal">equal</option>
7402 <option value="different">different</option>
7403 </param>
7404 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7405 </when>
7406 <when value="organelle">
7407 <param name="operation" type="select" label="Operator">
7408 <option value="equal">equal</option>
7409 <option value="different">different</option>
7410 </param>
7411 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7412 </when>
7413 <when value="serovar">
7414 <param name="operation" type="select" label="Operator">
7415 <option value="equal">equal</option>
7416 <option value="different">different</option>
7417 </param>
7418 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7419 </when>
7420 <when value="plasmid">
7421 <param name="operation" type="select" label="Operator">
7422 <option value="equal">equal</option>
7423 <option value="different">different</option>
7424 </param>
7425 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7426 </when>
7427 <when value="dataclass">
7428 <param name="operation" type="select" label="Operator">
7429 <option value="equal">equal</option>
7430 <option value="different">different</option>
7431 </param>
7432 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7433 </when>
7434 <when value="culture_collection">
7435 <param name="operation" type="select" label="Operator">
7436 <option value="equal">equal</option>
7437 <option value="different">different</option>
7438 </param>
7439 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7440 </when>
7441 </conditional>
7442 </repeat>
7443 <conditional name="display_opt">
7444 <param argument="--display" type="select" label="Display option to specify the display format">
7445 <expand macro="display_options"/>
7446 </param>
7447 <when value="xml">
7448 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
7449 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
7450 </when>
7451 <when value="text">
7452 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
7453 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
7454 </when>
7455 <when value="fastq"/>
7456 <when value="html">
7457 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
7458 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
7459 </when>
7460 <when value="report">
7461 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
7462 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
7463 <param argument="--fields" type="select" multiple="true" label="Fields to return">
7464 <option value="accession">accession</option>
7465 <option value="base_count">base_count</option>
7466 <option value="bio_material">bio_material</option>
7467 <option value="cell_line">cell_line</option>
7468 <option value="cell_type">cell_type</option>
7469 <option value="collected_by">collected_by</option>
7470 <option value="collection_date">collection_date</option>
7471 <option value="country">country</option>
7472 <option value="cultivar">cultivar</option>
7473 <option value="culture_collection">culture_collection</option>
7474 <option value="dataclass">dataclass</option>
7475 <option value="description">description</option>
7476 <option value="dev_stage">dev_stage</option>
7477 <option value="ecotype">ecotype</option>
7478 <option value="environmental_sample">environmental_sample</option>
7479 <option value="first_public">first_public</option>
7480 <option value="germline">germline</option>
7481 <option value="host">host</option>
7482 <option value="identified_by">identified_by</option>
7483 <option value="isolate">isolate</option>
7484 <option value="isolation_source">isolation_source</option>
7485 <option value="keywords">keywords</option>
7486 <option value="lab_host">lab_host</option>
7487 <option value="last_updated">last_updated</option>
7488 <option value="location">location</option>
7489 <option value="mating_type">mating_type</option>
7490 <option value="mol_type">mol_type</option>
7491 <option value="organelle">organelle</option>
7492 <option value="serotype">serotype</option>
7493 <option value="serovar">serovar</option>
7494 <option value="sex">sex</option>
7495 <option value="submitted_sex">submitted_sex</option>
7496 <option value="specimen_voucher">specimen_voucher</option>
7497 <option value="strain">strain</option>
7498 <option value="sub_species">sub_species</option>
7499 <option value="sub_strain">sub_strain</option>
7500 <option value="tax_division">tax_division</option>
7501 <option value="tissue_lib">tissue_lib</option>
7502 <option value="tissue_type">tissue_type</option>
7503 <option value="topology">topology</option>
7504 <option value="variety">variety</option>
7505 <option value="tax_id">tax_id</option>
7506 <option value="scientific_name">scientific_name</option>
7507 <option value="altitude">altitude</option>
7508 <option value="haplotype">haplotype</option>
7509 <option value="plasmid">plasmid</option>
7510 <option value="study_accession">study_accession</option>
7511 <option value="sequence_md5">sequence_md5</option>
7512 </param>
7513 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
7514 <option value="mol_type">in vivo molecule type of the sequence</option>
7515 <option value="last_updated">date when last updated</option>
7516 <option value="sequence_md5"></option>
7517 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
7518 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
7519 <option value="sex">sex of the organism from which the sample was obtained</option>
7520 <option value="keywords">keywords associated with sequence</option>
7521 <option value="collected_by">name of the person who collected the specimen</option>
7522 <option value="cell_line">cell line from which the sample was obtained</option>
7523 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
7524 <option value="bio_material">identifier for biological material including institute and collection code</option>
7525 <option value="identified_by">name of the taxonomist who identified the specimen</option>
7526 <option value="cell_type">cell type from which the sample was obtained</option>
7527 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
7528 <option value="tax_division">taxonomic division</option>
7529 <option value="collection_date">date that the specimen was collected</option>
7530 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
7531 <option value="altitude">Altitude (m)</option>
7532 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
7533 <option value="isolate">individual isolate from which sample was obtained</option>
7534 <option value="location">geographic location of isolation of the sample</option>
7535 <option value="study_accession">study accession number</option>
7536 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
7537 <option value="description">brief sequence description</option>
7538 <option value="accession">accession number</option>
7539 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
7540 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
7541 <option value="tissue_type">tissue type from which the sample was obtained</option>
7542 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
7543 <option value="tissue_lib">tissue library from which sample was obtained</option>
7544 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
7545 <option value="base_count">number of base pairs</option>
7546 <option value="topology">sequence topology: circular or linear</option>
7547 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
7548 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
7549 <option value="first_public">date when made public</option>
7550 <option value="strain">strain from which sample was obtained</option>
7551 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
7552 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
7553 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
7554 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
7555 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
7556 <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option>
7557 <option value="dataclass">sequence data class</option>
7558 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
7559 </param>
7560 </when>
7561 <when value="fasta"/>
7562 </conditional>
7563 </when>
7564 <when value="coding_update">
7565 <repeat name="queries" title="Add a query">
7566 <param name="combination_operation" type="select" label="Combination operation">
7567 <option value="AND">AND</option>
7568 <option value="OR">OR</option>
7569 <option value="NOT">NOT</option>
7570 </param>
7571 <conditional name="filter_field">
7572 <param name="field" type="select" label="Field to query">
7573 <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option>
7574 <option value="mol_type">in vivo molecule type of the sequence</option>
7575 <option value="last_updated">date when last updated</option>
7576 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
7577 <option value="transl_except">a single codon translation that does not conform to genetic code</option>
7578 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
7579 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
7580 <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option>
7581 <option value="sex">sex of the organism from which the sample was obtained</option>
7582 <option value="pseudo_gene">indicates that this feature is a pseudogene</option>
7583 <option value="standard_name">accepted standard name for a feature</option>
7584 <option value="collected_by">name of the person who collected the specimen</option>
7585 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
7586 <option value="cell_type">cell type from which the sample was obtained</option>
7587 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
7588 <option value="inference">a structured description of non-experimental evidence</option>
7589 <option value="bio_material">identifier for biological material including institute and collection code</option>
7590 <option value="parent_accession">parent sequence accession number</option>
7591 <option value="identified_by">name of the taxonomist who identified the specimen</option>
7592 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
7593 <option value="sequence_md5"></option>
7594 <option value="tax_division">taxonomic division</option>
7595 <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
7596 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
7597 <option value="altitude">Altitude (m)</option>
7598 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
7599 <option value="isolate">individual isolate from which sample was obtained</option>
7600 <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option>
7601 <option value="note">any comment or additional information</option>
7602 <option value="experiment">a brief description of the nature of the experimental evidence</option>
7603 <option value="location">geographic location of isolation of the sample</option>
7604 <option value="collection_date">date that the specimen was collected</option>
7605 <option value="allele">name of the allele for the given gene</option>
7606 <option value="protein_id">a stable protein identifier issued by INSDC</option>
7607 <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option>
7608 <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option>
7609 <option value="function">function attributed to a sequence</option>
7610 <option value="map">genomic map position of feature</option>
7611 <option value="product">name of the product associated with the feature</option>
7612 <option value="description">brief sequence description</option>
7613 <option value="cell_line">cell line from which the sample was obtained</option>
7614 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
7615 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
7616 <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option>
7617 <option value="accession">accession number</option>
7618 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
7619 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
7620 <option value="tissue_type">tissue type from which the sample was obtained</option>
7621 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
7622 <option value="tissue_lib">tissue library from which sample was obtained</option>
7623 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
7624 <option value="base_count">number of base pairs</option>
7625 <option value="topology">sequence topology: circular or linear</option>
7626 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
7627 <option value="first_public">date when made public</option>
7628 <option value="strain">strain from which sample was obtained</option>
7629 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
7630 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
7631 <option value="pseudo">the feature is non-functional</option>
7632 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
7633 <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option>
7634 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
7635 <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option>
7636 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
7637 <option value="keywords">keywords associated with sequence</option>
7638 <option value="dataclass">sequence data class</option>
7639 <option value="gene">symbol of the gene corresponding to a sequence region</option>
7640 <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option>
7641 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
7642 </param>
7643 <when value="operon">
7644 <param name="operation" type="select" label="Operator">
7645 <option value="equal">equal</option>
7646 <option value="different">different</option>
7647 </param>
7648 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7649 </when>
7650 <when value="mol_type">
7651 <param name="operation" type="select" label="Operator">
7652 <option value="equal">equal</option>
7653 <option value="different">different</option>
7654 </param>
7655 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7656 </when>
7657 <when value="last_updated">
7658 <param name="operation" type="select" label="Operator">
7659 <option value="equal">equal</option>
7660 <option value="different">different</option>
7661 <option value="lower">lower</option>
7662 <option value="equal or lower">equal or lower</option>
7663 <option value="higher">higher</option>
7664 <option value="equal or higher">equal or higher</option>
7665 </param>
7666 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
7667 </when>
7668 <when value="lab_host">
7669 <param name="operation" type="select" label="Operator">
7670 <option value="equal">equal</option>
7671 <option value="different">different</option>
7672 </param>
7673 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7674 </when>
7675 <when value="transl_except">
7676 <param name="operation" type="select" label="Operator">
7677 <option value="equal">equal</option>
7678 <option value="different">different</option>
7679 </param>
7680 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7681 </when>
7682 <when value="haplotype">
7683 <param name="operation" type="select" label="Operator">
7684 <option value="equal">equal</option>
7685 <option value="different">different</option>
7686 </param>
7687 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7688 </when>
7689 <when value="serotype">
7690 <param name="operation" type="select" label="Operator">
7691 <option value="equal">equal</option>
7692 <option value="different">different</option>
7693 </param>
7694 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7695 </when>
7696 <when value="trans_splicing">
7697 <param name="operation" type="select" label="Operator">
7698 <option value="equal">equal</option>
7699 </param>
7700 <param name="value" type="select" label="Value">
7701 <option value="yes">yes</option>
7702 <option value="true">true</option>
7703 <option value="no">no</option>
7704 <option value="false">false</option>
7705 </param>
7706 </when>
7707 <when value="sex">
7708 <param name="operation" type="select" label="Operator">
7709 <option value="equal">equal</option>
7710 <option value="different">different</option>
7711 </param>
7712 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7713 </when>
7714 <when value="pseudo_gene">
7715 <param name="operation" type="select" label="Operator">
7716 <option value="equal">equal</option>
7717 <option value="different">different</option>
7718 </param>
7719 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7720 </when>
7721 <when value="standard_name">
7722 <param name="operation" type="select" label="Operator">
7723 <option value="equal">equal</option>
7724 <option value="different">different</option>
7725 </param>
7726 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7727 </when>
7728 <when value="collected_by">
7729 <param name="operation" type="select" label="Operator">
7730 <option value="equal">equal</option>
7731 <option value="different">different</option>
7732 </param>
7733 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7734 </when>
7735 <when value="germline">
7736 <param name="operation" type="select" label="Operator">
7737 <option value="equal">equal</option>
7738 </param>
7739 <param name="value" type="select" label="Value">
7740 <option value="yes">yes</option>
7741 <option value="true">true</option>
7742 <option value="no">no</option>
7743 <option value="false">false</option>
7744 </param>
7745 </when>
7746 <when value="cell_type">
7747 <param name="operation" type="select" label="Operator">
7748 <option value="equal">equal</option>
7749 <option value="different">different</option>
7750 </param>
7751 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7752 </when>
7753 <when value="host">
7754 <param name="operation" type="select" label="Operator">
7755 <option value="equal">equal</option>
7756 <option value="different">different</option>
7757 </param>
7758 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7759 </when>
7760 <when value="inference">
7761 <param name="operation" type="select" label="Operator">
7762 <option value="equal">equal</option>
7763 <option value="different">different</option>
7764 </param>
7765 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7766 </when>
7767 <when value="bio_material">
7768 <param name="operation" type="select" label="Operator">
7769 <option value="equal">equal</option>
7770 <option value="different">different</option>
7771 </param>
7772 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7773 </when>
7774 <when value="parent_accession">
7775 <param name="operation" type="select" label="Operator">
7776 <option value="equal">equal</option>
7777 <option value="different">different</option>
7778 </param>
7779 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7780 </when>
7781 <when value="identified_by">
7782 <param name="operation" type="select" label="Operator">
7783 <option value="equal">equal</option>
7784 <option value="different">different</option>
7785 </param>
7786 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7787 </when>
7788 <when value="locus_tag">
7789 <param name="operation" type="select" label="Operator">
7790 <option value="equal">equal</option>
7791 <option value="different">different</option>
7792 </param>
7793 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7794 </when>
7795 <when value="sequence_md5">
7796 <param name="operation" type="select" label="Operator">
7797 <option value="equal">equal</option>
7798 <option value="different">different</option>
7799 </param>
7800 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7801 </when>
7802 <when value="tax_division">
7803 <param name="operation" type="select" label="Operator">
7804 <option value="equal">equal</option>
7805 <option value="different">different</option>
7806 </param>
7807 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7808 </when>
7809 <when value="old_locus_tag">
7810 <param name="operation" type="select" label="Operator">
7811 <option value="equal">equal</option>
7812 <option value="different">different</option>
7813 </param>
7814 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7815 </when>
7816 <when value="specimen_voucher">
7817 <param name="operation" type="select" label="Operator">
7818 <option value="equal">equal</option>
7819 <option value="different">different</option>
7820 </param>
7821 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7822 </when>
7823 <when value="altitude">
7824 <param name="operation" type="select" label="Operator">
7825 <option value="equal">equal</option>
7826 <option value="different">different</option>
7827 <option value="lower">lower</option>
7828 <option value="equal or lower">equal or lower</option>
7829 <option value="higher">higher</option>
7830 <option value="equal or higher">equal or higher</option>
7831 </param>
7832 <param name="value" type="float" value="" label="Any integer"/>
7833 </when>
7834 <when value="dev_stage">
7835 <param name="operation" type="select" label="Operator">
7836 <option value="equal">equal</option>
7837 <option value="different">different</option>
7838 </param>
7839 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7840 </when>
7841 <when value="isolate">
7842 <param name="operation" type="select" label="Operator">
7843 <option value="equal">equal</option>
7844 <option value="different">different</option>
7845 </param>
7846 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7847 </when>
7848 <when value="ec_number">
7849 <param name="operation" type="select" label="Operator">
7850 <option value="equal">equal</option>
7851 <option value="different">different</option>
7852 </param>
7853 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7854 </when>
7855 <when value="note">
7856 <param name="operation" type="select" label="Operator">
7857 <option value="equal">equal</option>
7858 <option value="different">different</option>
7859 </param>
7860 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7861 </when>
7862 <when value="experiment">
7863 <param name="operation" type="select" label="Operator">
7864 <option value="equal">equal</option>
7865 <option value="different">different</option>
7866 </param>
7867 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7868 </when>
7869 <when value="location">
7870 <conditional name="op">
7871 <param name="operation" type="select" label="Operation">
7872 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
7873 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
7874 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
7875 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
7876 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
7877 <option value="geo_point">An exact lat/lon position</option>
7878 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
7879 </param>
7880 <when value="geo_box2">
7881 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
7882 </when>
7883 <when value="geo_box1">
7884 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
7885 </when>
7886 <when value="geo_circ">
7887 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
7888 </when>
7889 <when value="geo_lat">
7890 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
7891 </when>
7892 <when value="geo_south">
7893 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
7894 </when>
7895 <when value="geo_point">
7896 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
7897 </when>
7898 <when value="geo_north">
7899 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
7900 </when>
7901 </conditional>
7902 </when>
7903 <when value="collection_date">
7904 <param name="operation" type="select" label="Operator">
7905 <option value="equal">equal</option>
7906 <option value="different">different</option>
7907 <option value="lower">lower</option>
7908 <option value="equal or lower">equal or lower</option>
7909 <option value="higher">higher</option>
7910 <option value="equal or higher">equal or higher</option>
7911 </param>
7912 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
7913 </when>
7914 <when value="allele">
7915 <param name="operation" type="select" label="Operator">
7916 <option value="equal">equal</option>
7917 <option value="different">different</option>
7918 </param>
7919 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7920 </when>
7921 <when value="protein_id">
7922 <param name="operation" type="select" label="Operator">
7923 <option value="equal">equal</option>
7924 <option value="different">different</option>
7925 </param>
7926 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7927 </when>
7928 <when value="partial">
7929 <param name="operation" type="select" label="Operator">
7930 <option value="equal">equal</option>
7931 </param>
7932 <param name="value" type="select" label="Value">
7933 <option value="yes">yes</option>
7934 <option value="true">true</option>
7935 <option value="no">no</option>
7936 <option value="false">false</option>
7937 </param>
7938 </when>
7939 <when value="artificial_location">
7940 <param name="operation" type="select" label="Operator">
7941 <option value="equal">equal</option>
7942 <option value="different">different</option>
7943 </param>
7944 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
7945 </when>
7946 <when value="function">
7947 <param name="operation" type="select" label="Operator">
7948 <option value="equal">equal</option>
7949 <option value="different">different</option>
7950 </param>
7951 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7952 </when>
7953 <when value="map">
7954 <param name="operation" type="select" label="Operator">
7955 <option value="equal">equal</option>
7956 <option value="different">different</option>
7957 </param>
7958 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7959 </when>
7960 <when value="product">
7961 <param name="operation" type="select" label="Operator">
7962 <option value="equal">equal</option>
7963 <option value="different">different</option>
7964 </param>
7965 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7966 </when>
7967 <when value="description">
7968 <param name="operation" type="select" label="Operator">
7969 <option value="equal">equal</option>
7970 <option value="different">different</option>
7971 </param>
7972 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7973 </when>
7974 <when value="cell_line">
7975 <param name="operation" type="select" label="Operator">
7976 <option value="equal">equal</option>
7977 <option value="different">different</option>
7978 </param>
7979 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7980 </when>
7981 <when value="gene_synonym">
7982 <param name="operation" type="select" label="Operator">
7983 <option value="equal">equal</option>
7984 <option value="different">different</option>
7985 </param>
7986 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7987 </when>
7988 <when value="ecotype">
7989 <param name="operation" type="select" label="Operator">
7990 <option value="equal">equal</option>
7991 <option value="different">different</option>
7992 </param>
7993 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
7994 </when>
7995 <when value="exception">
7996 <param name="operation" type="select" label="Operator">
7997 <option value="equal">equal</option>
7998 <option value="different">different</option>
7999 </param>
8000 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8001 </when>
8002 <when value="accession">
8003 <param name="operation" type="select" label="Operator">
8004 <option value="equal">equal</option>
8005 <option value="different">different</option>
8006 </param>
8007 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8008 </when>
8009 <when value="isolation_source">
8010 <param name="operation" type="select" label="Operator">
8011 <option value="equal">equal</option>
8012 <option value="different">different</option>
8013 </param>
8014 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8015 </when>
8016 <when value="mating_type">
8017 <param name="operation" type="select" label="Operator">
8018 <option value="equal">equal</option>
8019 <option value="different">different</option>
8020 </param>
8021 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8022 </when>
8023 <when value="tissue_type">
8024 <param name="operation" type="select" label="Operator">
8025 <option value="equal">equal</option>
8026 <option value="different">different</option>
8027 </param>
8028 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8029 </when>
8030 <when value="sub_strain">
8031 <param name="operation" type="select" label="Operator">
8032 <option value="equal">equal</option>
8033 <option value="different">different</option>
8034 </param>
8035 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8036 </when>
8037 <when value="tissue_lib">
8038 <param name="operation" type="select" label="Operator">
8039 <option value="equal">equal</option>
8040 <option value="different">different</option>
8041 </param>
8042 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8043 </when>
8044 <when value="cultivar">
8045 <param name="operation" type="select" label="Operator">
8046 <option value="equal">equal</option>
8047 <option value="different">different</option>
8048 </param>
8049 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8050 </when>
8051 <when value="base_count">
8052 <param name="operation" type="select" label="Operator">
8053 <option value="equal">equal</option>
8054 <option value="different">different</option>
8055 <option value="lower">lower</option>
8056 <option value="equal or lower">equal or lower</option>
8057 <option value="higher">higher</option>
8058 <option value="equal or higher">equal or higher</option>
8059 </param>
8060 <param name="value" type="float" value="" label="Any integer"/>
8061 </when>
8062 <when value="topology">
8063 <param name="operation" type="select" label="Operator">
8064 <option value="equal">equal</option>
8065 <option value="different">different</option>
8066 </param>
8067 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8068 </when>
8069 <when value="sub_species">
8070 <param name="operation" type="select" label="Operator">
8071 <option value="equal">equal</option>
8072 <option value="different">different</option>
8073 </param>
8074 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8075 </when>
8076 <when value="first_public">
8077 <param name="operation" type="select" label="Operator">
8078 <option value="equal">equal</option>
8079 <option value="different">different</option>
8080 <option value="lower">lower</option>
8081 <option value="equal or lower">equal or lower</option>
8082 <option value="higher">higher</option>
8083 <option value="equal or higher">equal or higher</option>
8084 </param>
8085 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
8086 </when>
8087 <when value="strain">
8088 <param name="operation" type="select" label="Operator">
8089 <option value="equal">equal</option>
8090 <option value="different">different</option>
8091 </param>
8092 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8093 </when>
8094 <when value="country">
8095 <param name="operation" type="select" label="Operator">
8096 <option value="equal">equal</option>
8097 <option value="different">different</option>
8098 </param>
8099 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8100 </when>
8101 <when value="variety">
8102 <param name="operation" type="select" label="Operator">
8103 <option value="equal">equal</option>
8104 <option value="different">different</option>
8105 </param>
8106 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8107 </when>
8108 <when value="pseudo">
8109 <param name="operation" type="select" label="Operator">
8110 <option value="equal">equal</option>
8111 </param>
8112 <param name="value" type="select" label="Value">
8113 <option value="yes">yes</option>
8114 <option value="true">true</option>
8115 <option value="no">no</option>
8116 <option value="false">false</option>
8117 </param>
8118 </when>
8119 <when value="environmental_sample">
8120 <param name="operation" type="select" label="Operator">
8121 <option value="equal">equal</option>
8122 </param>
8123 <param name="value" type="select" label="Value">
8124 <option value="yes">yes</option>
8125 <option value="true">true</option>
8126 <option value="no">no</option>
8127 <option value="false">false</option>
8128 </param>
8129 </when>
8130 <when value="transl_table">
8131 <param name="operation" type="select" label="Operator">
8132 <option value="equal">equal</option>
8133 <option value="different">different</option>
8134 </param>
8135 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8136 </when>
8137 <when value="organelle">
8138 <param name="operation" type="select" label="Operator">
8139 <option value="equal">equal</option>
8140 <option value="different">different</option>
8141 </param>
8142 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8143 </when>
8144 <when value="ribosomal_slippage">
8145 <param name="operation" type="select" label="Operator">
8146 <option value="equal">equal</option>
8147 </param>
8148 <param name="value" type="select" label="Value">
8149 <option value="yes">yes</option>
8150 <option value="true">true</option>
8151 <option value="no">no</option>
8152 <option value="false">false</option>
8153 </param>
8154 </when>
8155 <when value="serovar">
8156 <param name="operation" type="select" label="Operator">
8157 <option value="equal">equal</option>
8158 <option value="different">different</option>
8159 </param>
8160 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8161 </when>
8162 <when value="keywords">
8163 <param name="operation" type="select" label="Operator">
8164 <option value="equal">equal</option>
8165 <option value="different">different</option>
8166 </param>
8167 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8168 </when>
8169 <when value="dataclass">
8170 <param name="operation" type="select" label="Operator">
8171 <option value="equal">equal</option>
8172 <option value="different">different</option>
8173 </param>
8174 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8175 </when>
8176 <when value="gene">
8177 <param name="operation" type="select" label="Operator">
8178 <option value="equal">equal</option>
8179 <option value="different">different</option>
8180 </param>
8181 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8182 </when>
8183 <when value="codon_start">
8184 <param name="operation" type="select" label="Operator">
8185 <option value="equal">equal</option>
8186 <option value="different">different</option>
8187 </param>
8188 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8189 </when>
8190 <when value="culture_collection">
8191 <param name="operation" type="select" label="Operator">
8192 <option value="equal">equal</option>
8193 <option value="different">different</option>
8194 </param>
8195 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8196 </when>
8197 </conditional>
8198 </repeat>
8199 <conditional name="display_opt">
8200 <param argument="--display" type="select" label="Display option to specify the display format">
8201 <expand macro="display_options"/>
8202 </param>
8203 <when value="xml">
8204 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8205 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8206 </when>
8207 <when value="text">
8208 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8209 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8210 </when>
8211 <when value="fastq"/>
8212 <when value="html">
8213 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8214 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8215 </when>
8216 <when value="report">
8217 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8218 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8219 <param argument="--fields" type="select" multiple="true" label="Fields to return">
8220 <option value="accession">accession</option>
8221 <option value="base_count">base_count</option>
8222 <option value="bio_material">bio_material</option>
8223 <option value="cell_line">cell_line</option>
8224 <option value="cell_type">cell_type</option>
8225 <option value="collected_by">collected_by</option>
8226 <option value="collection_date">collection_date</option>
8227 <option value="country">country</option>
8228 <option value="cultivar">cultivar</option>
8229 <option value="culture_collection">culture_collection</option>
8230 <option value="dataclass">dataclass</option>
8231 <option value="description">description</option>
8232 <option value="dev_stage">dev_stage</option>
8233 <option value="ecotype">ecotype</option>
8234 <option value="environmental_sample">environmental_sample</option>
8235 <option value="first_public">first_public</option>
8236 <option value="germline">germline</option>
8237 <option value="host">host</option>
8238 <option value="identified_by">identified_by</option>
8239 <option value="isolate">isolate</option>
8240 <option value="isolation_source">isolation_source</option>
8241 <option value="keywords">keywords</option>
8242 <option value="lab_host">lab_host</option>
8243 <option value="last_updated">last_updated</option>
8244 <option value="location">location</option>
8245 <option value="mating_type">mating_type</option>
8246 <option value="mol_type">mol_type</option>
8247 <option value="organelle">organelle</option>
8248 <option value="serotype">serotype</option>
8249 <option value="serovar">serovar</option>
8250 <option value="sex">sex</option>
8251 <option value="submitted_sex">submitted_sex</option>
8252 <option value="specimen_voucher">specimen_voucher</option>
8253 <option value="strain">strain</option>
8254 <option value="sub_species">sub_species</option>
8255 <option value="sub_strain">sub_strain</option>
8256 <option value="tax_division">tax_division</option>
8257 <option value="tissue_lib">tissue_lib</option>
8258 <option value="tissue_type">tissue_type</option>
8259 <option value="variety">variety</option>
8260 <option value="allele">allele</option>
8261 <option value="artificial_location">artificial_location</option>
8262 <option value="codon_start">codon_start</option>
8263 <option value="ec_number">ec_number</option>
8264 <option value="exception">exception</option>
8265 <option value="experiment">experiment</option>
8266 <option value="function">function</option>
8267 <option value="topology">topology</option>
8268 <option value="gene">gene</option>
8269 <option value="gene_synonym">gene_synonym</option>
8270 <option value="inference">inference</option>
8271 <option value="locus_tag">locus_tag</option>
8272 <option value="map">map</option>
8273 <option value="note">note</option>
8274 <option value="old_locus_tag">old_locus_tag</option>
8275 <option value="operon">operon</option>
8276 <option value="partial">partial</option>
8277 <option value="product">product</option>
8278 <option value="protein_id">protein_id</option>
8279 <option value="pseudo">pseudo</option>
8280 <option value="pseudo_gene">pseudo_gene</option>
8281 <option value="ribosomal_slippage">ribosomal_slippage</option>
8282 <option value="standard_name">standard_name</option>
8283 <option value="trans_splicing">trans_splicing</option>
8284 <option value="transl_except">transl_except</option>
8285 <option value="transl_table">transl_table</option>
8286 <option value="tax_id">tax_id</option>
8287 <option value="scientific_name">scientific_name</option>
8288 <option value="parent_accession">parent_accession</option>
8289 <option value="altitude">altitude</option>
8290 <option value="haplotype">haplotype</option>
8291 <option value="sequence_md5">sequence_md5</option>
8292 </param>
8293 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
8294 <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option>
8295 <option value="mol_type">in vivo molecule type of the sequence</option>
8296 <option value="last_updated">date when last updated</option>
8297 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
8298 <option value="transl_except">a single codon translation that does not conform to genetic code</option>
8299 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
8300 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
8301 <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option>
8302 <option value="sex">sex of the organism from which the sample was obtained</option>
8303 <option value="pseudo_gene">indicates that this feature is a pseudogene</option>
8304 <option value="standard_name">accepted standard name for a feature</option>
8305 <option value="collected_by">name of the person who collected the specimen</option>
8306 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
8307 <option value="cell_type">cell type from which the sample was obtained</option>
8308 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
8309 <option value="inference">a structured description of non-experimental evidence</option>
8310 <option value="bio_material">identifier for biological material including institute and collection code</option>
8311 <option value="parent_accession">parent sequence accession number</option>
8312 <option value="identified_by">name of the taxonomist who identified the specimen</option>
8313 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
8314 <option value="sequence_md5"></option>
8315 <option value="tax_division">taxonomic division</option>
8316 <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
8317 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
8318 <option value="altitude">Altitude (m)</option>
8319 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
8320 <option value="isolate">individual isolate from which sample was obtained</option>
8321 <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option>
8322 <option value="note">any comment or additional information</option>
8323 <option value="experiment">a brief description of the nature of the experimental evidence</option>
8324 <option value="location">geographic location of isolation of the sample</option>
8325 <option value="collection_date">date that the specimen was collected</option>
8326 <option value="allele">name of the allele for the given gene</option>
8327 <option value="protein_id">a stable protein identifier issued by INSDC</option>
8328 <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option>
8329 <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option>
8330 <option value="function">function attributed to a sequence</option>
8331 <option value="map">genomic map position of feature</option>
8332 <option value="product">name of the product associated with the feature</option>
8333 <option value="description">brief sequence description</option>
8334 <option value="cell_line">cell line from which the sample was obtained</option>
8335 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
8336 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
8337 <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option>
8338 <option value="accession">accession number</option>
8339 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
8340 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
8341 <option value="tissue_type">tissue type from which the sample was obtained</option>
8342 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
8343 <option value="tissue_lib">tissue library from which sample was obtained</option>
8344 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
8345 <option value="base_count">number of base pairs</option>
8346 <option value="topology">sequence topology: circular or linear</option>
8347 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
8348 <option value="first_public">date when made public</option>
8349 <option value="strain">strain from which sample was obtained</option>
8350 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
8351 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
8352 <option value="pseudo">the feature is non-functional</option>
8353 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
8354 <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option>
8355 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
8356 <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option>
8357 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
8358 <option value="keywords">keywords associated with sequence</option>
8359 <option value="dataclass">sequence data class</option>
8360 <option value="gene">symbol of the gene corresponding to a sequence region</option>
8361 <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option>
8362 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
8363 </param>
8364 </when>
8365 <when value="fasta"/>
8366 </conditional>
8367 </when>
8368 <when value="tsa_set">
8369 <repeat name="queries" title="Add a query">
8370 <param name="combination_operation" type="select" label="Combination operation">
8371 <option value="AND">AND</option>
8372 <option value="OR">OR</option>
8373 <option value="NOT">NOT</option>
8374 </param>
8375 <conditional name="filter_field">
8376 <param name="field" type="select" label="Field to query">
8377 <option value="mol_type">in vivo molecule type of the sequence</option>
8378 <option value="last_updated">date when last updated</option>
8379 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
8380 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
8381 <option value="accession">accession number</option>
8382 <option value="sex">sex of the organism from which the sample was obtained</option>
8383 <option value="cell_line">cell line from which the sample was obtained</option>
8384 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
8385 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
8386 <option value="bio_material">identifier for biological material including institute and collection code</option>
8387 <option value="identified_by">name of the taxonomist who identified the specimen</option>
8388 <option value="cell_type">cell type from which the sample was obtained</option>
8389 <option value="tax_division">taxonomic division</option>
8390 <option value="collection_date">date that the specimen was collected</option>
8391 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
8392 <option value="altitude">Altitude (m)</option>
8393 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
8394 <option value="isolate">individual isolate from which sample was obtained</option>
8395 <option value="location">geographic location of isolation of the sample</option>
8396 <option value="study_accession">study accession number</option>
8397 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
8398 <option value="description">brief sequence description</option>
8399 <option value="tissue_lib">tissue library from which sample was obtained</option>
8400 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
8401 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
8402 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
8403 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
8404 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
8405 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
8406 <option value="collected_by">name of the person who collected the specimen</option>
8407 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
8408 <option value="first_public">date when made public</option>
8409 <option value="strain">strain from which sample was obtained</option>
8410 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
8411 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
8412 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
8413 <option value="tissue_type">tissue type from which the sample was obtained</option>
8414 <option value="keywords">keywords associated with sequence</option>
8415 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
8416 </param>
8417 <when value="mol_type">
8418 <param name="operation" type="select" label="Operator">
8419 <option value="equal">equal</option>
8420 <option value="different">different</option>
8421 </param>
8422 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8423 </when>
8424 <when value="last_updated">
8425 <param name="operation" type="select" label="Operator">
8426 <option value="equal">equal</option>
8427 <option value="different">different</option>
8428 <option value="lower">lower</option>
8429 <option value="equal or lower">equal or lower</option>
8430 <option value="higher">higher</option>
8431 <option value="equal or higher">equal or higher</option>
8432 </param>
8433 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
8434 </when>
8435 <when value="lab_host">
8436 <param name="operation" type="select" label="Operator">
8437 <option value="equal">equal</option>
8438 <option value="different">different</option>
8439 </param>
8440 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8441 </when>
8442 <when value="haplotype">
8443 <param name="operation" type="select" label="Operator">
8444 <option value="equal">equal</option>
8445 <option value="different">different</option>
8446 </param>
8447 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8448 </when>
8449 <when value="accession">
8450 <param name="operation" type="select" label="Operator">
8451 <option value="equal">equal</option>
8452 <option value="different">different</option>
8453 </param>
8454 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8455 </when>
8456 <when value="sex">
8457 <param name="operation" type="select" label="Operator">
8458 <option value="equal">equal</option>
8459 <option value="different">different</option>
8460 </param>
8461 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8462 </when>
8463 <when value="cell_line">
8464 <param name="operation" type="select" label="Operator">
8465 <option value="equal">equal</option>
8466 <option value="different">different</option>
8467 </param>
8468 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8469 </when>
8470 <when value="host">
8471 <param name="operation" type="select" label="Operator">
8472 <option value="equal">equal</option>
8473 <option value="different">different</option>
8474 </param>
8475 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8476 </when>
8477 <when value="ecotype">
8478 <param name="operation" type="select" label="Operator">
8479 <option value="equal">equal</option>
8480 <option value="different">different</option>
8481 </param>
8482 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8483 </when>
8484 <when value="bio_material">
8485 <param name="operation" type="select" label="Operator">
8486 <option value="equal">equal</option>
8487 <option value="different">different</option>
8488 </param>
8489 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8490 </when>
8491 <when value="identified_by">
8492 <param name="operation" type="select" label="Operator">
8493 <option value="equal">equal</option>
8494 <option value="different">different</option>
8495 </param>
8496 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8497 </when>
8498 <when value="cell_type">
8499 <param name="operation" type="select" label="Operator">
8500 <option value="equal">equal</option>
8501 <option value="different">different</option>
8502 </param>
8503 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8504 </when>
8505 <when value="tax_division">
8506 <param name="operation" type="select" label="Operator">
8507 <option value="equal">equal</option>
8508 <option value="different">different</option>
8509 </param>
8510 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
8511 </when>
8512 <when value="collection_date">
8513 <param name="operation" type="select" label="Operator">
8514 <option value="equal">equal</option>
8515 <option value="different">different</option>
8516 <option value="lower">lower</option>
8517 <option value="equal or lower">equal or lower</option>
8518 <option value="higher">higher</option>
8519 <option value="equal or higher">equal or higher</option>
8520 </param>
8521 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
8522 </when>
8523 <when value="specimen_voucher">
8524 <param name="operation" type="select" label="Operator">
8525 <option value="equal">equal</option>
8526 <option value="different">different</option>
8527 </param>
8528 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8529 </when>
8530 <when value="altitude">
8531 <param name="operation" type="select" label="Operator">
8532 <option value="equal">equal</option>
8533 <option value="different">different</option>
8534 <option value="lower">lower</option>
8535 <option value="equal or lower">equal or lower</option>
8536 <option value="higher">higher</option>
8537 <option value="equal or higher">equal or higher</option>
8538 </param>
8539 <param name="value" type="float" value="" label="Any integer"/>
8540 </when>
8541 <when value="dev_stage">
8542 <param name="operation" type="select" label="Operator">
8543 <option value="equal">equal</option>
8544 <option value="different">different</option>
8545 </param>
8546 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8547 </when>
8548 <when value="isolate">
8549 <param name="operation" type="select" label="Operator">
8550 <option value="equal">equal</option>
8551 <option value="different">different</option>
8552 </param>
8553 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8554 </when>
8555 <when value="location">
8556 <conditional name="op">
8557 <param name="operation" type="select" label="Operation">
8558 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
8559 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
8560 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
8561 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
8562 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
8563 <option value="geo_point">An exact lat/lon position</option>
8564 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
8565 </param>
8566 <when value="geo_box2">
8567 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
8568 </when>
8569 <when value="geo_box1">
8570 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
8571 </when>
8572 <when value="geo_circ">
8573 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
8574 </when>
8575 <when value="geo_lat">
8576 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
8577 </when>
8578 <when value="geo_south">
8579 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
8580 </when>
8581 <when value="geo_point">
8582 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
8583 </when>
8584 <when value="geo_north">
8585 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
8586 </when>
8587 </conditional>
8588 </when>
8589 <when value="study_accession">
8590 <param name="operation" type="select" label="Operator">
8591 <option value="equal">equal</option>
8592 <option value="different">different</option>
8593 </param>
8594 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8595 </when>
8596 <when value="germline">
8597 <param name="operation" type="select" label="Operator">
8598 <option value="equal">equal</option>
8599 </param>
8600 <param name="value" type="select" label="Value">
8601 <option value="yes">yes</option>
8602 <option value="true">true</option>
8603 <option value="no">no</option>
8604 <option value="false">false</option>
8605 </param>
8606 </when>
8607 <when value="description">
8608 <param name="operation" type="select" label="Operator">
8609 <option value="equal">equal</option>
8610 <option value="different">different</option>
8611 </param>
8612 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8613 </when>
8614 <when value="tissue_lib">
8615 <param name="operation" type="select" label="Operator">
8616 <option value="equal">equal</option>
8617 <option value="different">different</option>
8618 </param>
8619 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8620 </when>
8621 <when value="isolation_source">
8622 <param name="operation" type="select" label="Operator">
8623 <option value="equal">equal</option>
8624 <option value="different">different</option>
8625 </param>
8626 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8627 </when>
8628 <when value="mating_type">
8629 <param name="operation" type="select" label="Operator">
8630 <option value="equal">equal</option>
8631 <option value="different">different</option>
8632 </param>
8633 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8634 </when>
8635 <when value="serovar">
8636 <param name="operation" type="select" label="Operator">
8637 <option value="equal">equal</option>
8638 <option value="different">different</option>
8639 </param>
8640 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8641 </when>
8642 <when value="serotype">
8643 <param name="operation" type="select" label="Operator">
8644 <option value="equal">equal</option>
8645 <option value="different">different</option>
8646 </param>
8647 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8648 </when>
8649 <when value="sub_strain">
8650 <param name="operation" type="select" label="Operator">
8651 <option value="equal">equal</option>
8652 <option value="different">different</option>
8653 </param>
8654 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8655 </when>
8656 <when value="cultivar">
8657 <param name="operation" type="select" label="Operator">
8658 <option value="equal">equal</option>
8659 <option value="different">different</option>
8660 </param>
8661 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8662 </when>
8663 <when value="collected_by">
8664 <param name="operation" type="select" label="Operator">
8665 <option value="equal">equal</option>
8666 <option value="different">different</option>
8667 </param>
8668 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8669 </when>
8670 <when value="sub_species">
8671 <param name="operation" type="select" label="Operator">
8672 <option value="equal">equal</option>
8673 <option value="different">different</option>
8674 </param>
8675 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8676 </when>
8677 <when value="first_public">
8678 <param name="operation" type="select" label="Operator">
8679 <option value="equal">equal</option>
8680 <option value="different">different</option>
8681 <option value="lower">lower</option>
8682 <option value="equal or lower">equal or lower</option>
8683 <option value="higher">higher</option>
8684 <option value="equal or higher">equal or higher</option>
8685 </param>
8686 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
8687 </when>
8688 <when value="strain">
8689 <param name="operation" type="select" label="Operator">
8690 <option value="equal">equal</option>
8691 <option value="different">different</option>
8692 </param>
8693 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8694 </when>
8695 <when value="country">
8696 <param name="operation" type="select" label="Operator">
8697 <option value="equal">equal</option>
8698 <option value="different">different</option>
8699 </param>
8700 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8701 </when>
8702 <when value="variety">
8703 <param name="operation" type="select" label="Operator">
8704 <option value="equal">equal</option>
8705 <option value="different">different</option>
8706 </param>
8707 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8708 </when>
8709 <when value="environmental_sample">
8710 <param name="operation" type="select" label="Operator">
8711 <option value="equal">equal</option>
8712 </param>
8713 <param name="value" type="select" label="Value">
8714 <option value="yes">yes</option>
8715 <option value="true">true</option>
8716 <option value="no">no</option>
8717 <option value="false">false</option>
8718 </param>
8719 </when>
8720 <when value="tissue_type">
8721 <param name="operation" type="select" label="Operator">
8722 <option value="equal">equal</option>
8723 <option value="different">different</option>
8724 </param>
8725 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8726 </when>
8727 <when value="keywords">
8728 <param name="operation" type="select" label="Operator">
8729 <option value="equal">equal</option>
8730 <option value="different">different</option>
8731 </param>
8732 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8733 </when>
8734 <when value="culture_collection">
8735 <param name="operation" type="select" label="Operator">
8736 <option value="equal">equal</option>
8737 <option value="different">different</option>
8738 </param>
8739 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8740 </when>
8741 </conditional>
8742 </repeat>
8743 <conditional name="display_opt">
8744 <param argument="--display" type="select" label="Display option to specify the display format">
8745 <expand macro="display_options"/>
8746 </param>
8747 <when value="xml">
8748 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8749 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8750 </when>
8751 <when value="text">
8752 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8753 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8754 </when>
8755 <when value="fastq"/>
8756 <when value="html">
8757 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8758 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8759 </when>
8760 <when value="report">
8761 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8762 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8763 <param argument="--fields" type="select" multiple="true" label="Fields to return">
8764 <option value="accession">accession</option>
8765 <option value="bio_material">bio_material</option>
8766 <option value="cell_line">cell_line</option>
8767 <option value="cell_type">cell_type</option>
8768 <option value="collected_by">collected_by</option>
8769 <option value="collection_date">collection_date</option>
8770 <option value="country">country</option>
8771 <option value="cultivar">cultivar</option>
8772 <option value="culture_collection">culture_collection</option>
8773 <option value="description">description</option>
8774 <option value="dev_stage">dev_stage</option>
8775 <option value="ecotype">ecotype</option>
8776 <option value="environmental_sample">environmental_sample</option>
8777 <option value="first_public">first_public</option>
8778 <option value="germline">germline</option>
8779 <option value="host">host</option>
8780 <option value="identified_by">identified_by</option>
8781 <option value="isolate">isolate</option>
8782 <option value="isolation_source">isolation_source</option>
8783 <option value="keywords">keywords</option>
8784 <option value="lab_host">lab_host</option>
8785 <option value="last_updated">last_updated</option>
8786 <option value="location">location</option>
8787 <option value="mating_type">mating_type</option>
8788 <option value="mol_type">mol_type</option>
8789 <option value="serotype">serotype</option>
8790 <option value="serovar">serovar</option>
8791 <option value="sex">sex</option>
8792 <option value="submitted_sex">submitted_sex</option>
8793 <option value="specimen_voucher">specimen_voucher</option>
8794 <option value="strain">strain</option>
8795 <option value="sub_species">sub_species</option>
8796 <option value="sub_strain">sub_strain</option>
8797 <option value="tax_division">tax_division</option>
8798 <option value="tissue_lib">tissue_lib</option>
8799 <option value="tissue_type">tissue_type</option>
8800 <option value="variety">variety</option>
8801 <option value="tax_id">tax_id</option>
8802 <option value="scientific_name">scientific_name</option>
8803 <option value="altitude">altitude</option>
8804 <option value="haplotype">haplotype</option>
8805 <option value="study_accession">study_accession</option>
8806 <option value="set_files">set_files</option>
8807 </param>
8808 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
8809 <option value="mol_type">in vivo molecule type of the sequence</option>
8810 <option value="last_updated">date when last updated</option>
8811 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
8812 <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option>
8813 <option value="accession">accession number</option>
8814 <option value="sex">sex of the organism from which the sample was obtained</option>
8815 <option value="cell_line">cell line from which the sample was obtained</option>
8816 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
8817 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
8818 <option value="bio_material">identifier for biological material including institute and collection code</option>
8819 <option value="identified_by">name of the taxonomist who identified the specimen</option>
8820 <option value="cell_type">cell type from which the sample was obtained</option>
8821 <option value="tax_division">taxonomic division</option>
8822 <option value="collection_date">date that the specimen was collected</option>
8823 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
8824 <option value="altitude">Altitude (m)</option>
8825 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
8826 <option value="isolate">individual isolate from which sample was obtained</option>
8827 <option value="location">geographic location of isolation of the sample</option>
8828 <option value="study_accession">study accession number</option>
8829 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
8830 <option value="description">brief sequence description</option>
8831 <option value="tissue_lib">tissue library from which sample was obtained</option>
8832 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
8833 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
8834 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
8835 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
8836 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
8837 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
8838 <option value="collected_by">name of the person who collected the specimen</option>
8839 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
8840 <option value="first_public">date when made public</option>
8841 <option value="strain">strain from which sample was obtained</option>
8842 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
8843 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
8844 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
8845 <option value="tissue_type">tissue type from which the sample was obtained</option>
8846 <option value="keywords">keywords associated with sequence</option>
8847 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
8848 </param>
8849 </when>
8850 <when value="fasta"/>
8851 </conditional>
8852 </when>
8853 <when value="analysis_study">
8854 <repeat name="queries" title="Add a query">
8855 <param name="combination_operation" type="select" label="Combination operation">
8856 <option value="AND">AND</option>
8857 <option value="OR">OR</option>
8858 <option value="NOT">NOT</option>
8859 </param>
8860 <conditional name="filter_field">
8861 <param name="field" type="select" label="Field to query">
8862 <option value="study_title">brief sequencing study description</option>
8863 <option value="secondary_study_accession">project accession number</option>
8864 <option value="study_alias">submitter's name for the study</option>
8865 <option value="study_accession">study accession number</option>
8866 </param>
8867 <when value="study_title">
8868 <param name="operation" type="select" label="Operator">
8869 <option value="equal">equal</option>
8870 <option value="different">different</option>
8871 </param>
8872 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8873 </when>
8874 <when value="secondary_study_accession">
8875 <param name="operation" type="select" label="Operator">
8876 <option value="equal">equal</option>
8877 <option value="different">different</option>
8878 </param>
8879 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8880 </when>
8881 <when value="study_alias">
8882 <param name="operation" type="select" label="Operator">
8883 <option value="equal">equal</option>
8884 <option value="different">different</option>
8885 </param>
8886 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8887 </when>
8888 <when value="study_accession">
8889 <param name="operation" type="select" label="Operator">
8890 <option value="equal">equal</option>
8891 <option value="different">different</option>
8892 </param>
8893 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
8894 </when>
8895 </conditional>
8896 </repeat>
8897 <conditional name="display_opt">
8898 <param argument="--display" type="select" label="Display option to specify the display format">
8899 <expand macro="display_options"/>
8900 </param>
8901 <when value="xml">
8902 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8903 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8904 </when>
8905 <when value="text">
8906 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8907 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8908 </when>
8909 <when value="fastq"/>
8910 <when value="html">
8911 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8912 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8913 </when>
8914 <when value="report">
8915 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
8916 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
8917 <param argument="--fields" type="select" multiple="true" label="Fields to return">
8918 <option value="study_accession">study_accession</option>
8919 <option value="secondary_study_accession">secondary_study_accession</option>
8920 <option value="study_title">study_title</option>
8921 <option value="study_alias">study_alias</option>
8922 </param>
8923 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
8924 <option value="study_title">brief sequencing study description</option>
8925 <option value="secondary_study_accession">project accession number</option>
8926 <option value="study_alias">submitter's name for the study</option>
8927 <option value="study_accession">study accession number</option>
8928 </param>
8929 </when>
8930 <when value="fasta"/>
8931 </conditional>
8932 </when>
8933 <when value="noncoding_update">
8934 <repeat name="queries" title="Add a query">
8935 <param name="combination_operation" type="select" label="Combination operation">
8936 <option value="AND">AND</option>
8937 <option value="OR">OR</option>
8938 <option value="NOT">NOT</option>
8939 </param>
8940 <conditional name="filter_field">
8941 <param name="field" type="select" label="Field to query">
8942 <option value="mol_type">in vivo molecule type of the sequence</option>
8943 <option value="last_updated">date when last updated</option>
8944 <option value="sequence_md5"></option>
8945 <option value="collected_by">name of the person who collected the specimen</option>
8946 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
8947 <option value="sex">sex of the organism from which the sample was obtained</option>
8948 <option value="keywords">keywords associated with sequence</option>
8949 <option value="cell_line">cell line from which the sample was obtained</option>
8950 <option value="inference">a structured description of non-experimental evidence</option>
8951 <option value="bio_material">identifier for biological material including institute and collection code</option>
8952 <option value="identified_by">name of the taxonomist who identified the specimen</option>
8953 <option value="note">any comment or additional information</option>
8954 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
8955 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
8956 <option value="tax_division">taxonomic division</option>
8957 <option value="collection_date">date that the specimen was collected</option>
8958 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
8959 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
8960 <option value="isolate">individual isolate from which sample was obtained</option>
8961 <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option>
8962 <option value="experiment">a brief description of the nature of the experimental evidence</option>
8963 <option value="location">geographic location of isolation of the sample</option>
8964 <option value="study_accession">study accession number</option>
8965 <option value="function">function attributed to a sequence</option>
8966 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
8967 <option value="product">name of the product associated with the feature</option>
8968 <option value="description">brief sequence description</option>
8969 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
8970 <option value="cell_type">cell type from which the sample was obtained</option>
8971 <option value="accession">accession number</option>
8972 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
8973 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
8974 <option value="tissue_type">tissue type from which the sample was obtained</option>
8975 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
8976 <option value="tissue_lib">tissue library from which sample was obtained</option>
8977 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
8978 <option value="base_count">number of base pairs</option>
8979 <option value="topology">sequence topology: circular or linear</option>
8980 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
8981 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
8982 <option value="first_public">date when made public</option>
8983 <option value="strain">strain from which sample was obtained</option>
8984 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
8985 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
8986 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
8987 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
8988 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
8989 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
8990 <option value="rna_class">classification of RNA</option>
8991 <option value="dataclass">sequence data class</option>
8992 <option value="gene">symbol of the gene corresponding to a sequence region</option>
8993 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
8994 </param>
8995 <when value="mol_type">
8996 <param name="operation" type="select" label="Operator">
8997 <option value="equal">equal</option>
8998 <option value="different">different</option>
8999 </param>
9000 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9001 </when>
9002 <when value="last_updated">
9003 <param name="operation" type="select" label="Operator">
9004 <option value="equal">equal</option>
9005 <option value="different">different</option>
9006 <option value="lower">lower</option>
9007 <option value="equal or lower">equal or lower</option>
9008 <option value="higher">higher</option>
9009 <option value="equal or higher">equal or higher</option>
9010 </param>
9011 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
9012 </when>
9013 <when value="sequence_md5">
9014 <param name="operation" type="select" label="Operator">
9015 <option value="equal">equal</option>
9016 <option value="different">different</option>
9017 </param>
9018 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9019 </when>
9020 <when value="collected_by">
9021 <param name="operation" type="select" label="Operator">
9022 <option value="equal">equal</option>
9023 <option value="different">different</option>
9024 </param>
9025 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9026 </when>
9027 <when value="serotype">
9028 <param name="operation" type="select" label="Operator">
9029 <option value="equal">equal</option>
9030 <option value="different">different</option>
9031 </param>
9032 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9033 </when>
9034 <when value="sex">
9035 <param name="operation" type="select" label="Operator">
9036 <option value="equal">equal</option>
9037 <option value="different">different</option>
9038 </param>
9039 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9040 </when>
9041 <when value="keywords">
9042 <param name="operation" type="select" label="Operator">
9043 <option value="equal">equal</option>
9044 <option value="different">different</option>
9045 </param>
9046 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9047 </when>
9048 <when value="cell_line">
9049 <param name="operation" type="select" label="Operator">
9050 <option value="equal">equal</option>
9051 <option value="different">different</option>
9052 </param>
9053 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9054 </when>
9055 <when value="inference">
9056 <param name="operation" type="select" label="Operator">
9057 <option value="equal">equal</option>
9058 <option value="different">different</option>
9059 </param>
9060 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9061 </when>
9062 <when value="bio_material">
9063 <param name="operation" type="select" label="Operator">
9064 <option value="equal">equal</option>
9065 <option value="different">different</option>
9066 </param>
9067 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9068 </when>
9069 <when value="identified_by">
9070 <param name="operation" type="select" label="Operator">
9071 <option value="equal">equal</option>
9072 <option value="different">different</option>
9073 </param>
9074 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9075 </when>
9076 <when value="note">
9077 <param name="operation" type="select" label="Operator">
9078 <option value="equal">equal</option>
9079 <option value="different">different</option>
9080 </param>
9081 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9082 </when>
9083 <when value="locus_tag">
9084 <param name="operation" type="select" label="Operator">
9085 <option value="equal">equal</option>
9086 <option value="different">different</option>
9087 </param>
9088 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9089 </when>
9090 <when value="lab_host">
9091 <param name="operation" type="select" label="Operator">
9092 <option value="equal">equal</option>
9093 <option value="different">different</option>
9094 </param>
9095 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9096 </when>
9097 <when value="tax_division">
9098 <param name="operation" type="select" label="Operator">
9099 <option value="equal">equal</option>
9100 <option value="different">different</option>
9101 </param>
9102 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9103 </when>
9104 <when value="collection_date">
9105 <param name="operation" type="select" label="Operator">
9106 <option value="equal">equal</option>
9107 <option value="different">different</option>
9108 <option value="lower">lower</option>
9109 <option value="equal or lower">equal or lower</option>
9110 <option value="higher">higher</option>
9111 <option value="equal or higher">equal or higher</option>
9112 </param>
9113 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
9114 </when>
9115 <when value="specimen_voucher">
9116 <param name="operation" type="select" label="Operator">
9117 <option value="equal">equal</option>
9118 <option value="different">different</option>
9119 </param>
9120 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9121 </when>
9122 <when value="dev_stage">
9123 <param name="operation" type="select" label="Operator">
9124 <option value="equal">equal</option>
9125 <option value="different">different</option>
9126 </param>
9127 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9128 </when>
9129 <when value="isolate">
9130 <param name="operation" type="select" label="Operator">
9131 <option value="equal">equal</option>
9132 <option value="different">different</option>
9133 </param>
9134 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9135 </when>
9136 <when value="anticodon">
9137 <param name="operation" type="select" label="Operator">
9138 <option value="equal">equal</option>
9139 <option value="different">different</option>
9140 </param>
9141 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9142 </when>
9143 <when value="experiment">
9144 <param name="operation" type="select" label="Operator">
9145 <option value="equal">equal</option>
9146 <option value="different">different</option>
9147 </param>
9148 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9149 </when>
9150 <when value="location">
9151 <conditional name="op">
9152 <param name="operation" type="select" label="Operation">
9153 <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option>
9154 <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option>
9155 <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option>
9156 <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option>
9157 <option value="geo_south">All locations south of a given latitude (inclusive).</option>
9158 <option value="geo_point">An exact lat/lon position</option>
9159 <option value="geo_north">All locations north of a given latitude (inclusive).</option>
9160 </param>
9161 <when value="geo_box2">
9162 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
9163 </when>
9164 <when value="geo_box1">
9165 <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/>
9166 </when>
9167 <when value="geo_circ">
9168 <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/>
9169 </when>
9170 <when value="geo_lat">
9171 <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/>
9172 </when>
9173 <when value="geo_south">
9174 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
9175 </when>
9176 <when value="geo_point">
9177 <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/>
9178 </when>
9179 <when value="geo_north">
9180 <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/>
9181 </when>
9182 </conditional>
9183 </when>
9184 <when value="study_accession">
9185 <param name="operation" type="select" label="Operator">
9186 <option value="equal">equal</option>
9187 <option value="different">different</option>
9188 </param>
9189 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9190 </when>
9191 <when value="function">
9192 <param name="operation" type="select" label="Operator">
9193 <option value="equal">equal</option>
9194 <option value="different">different</option>
9195 </param>
9196 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9197 </when>
9198 <when value="germline">
9199 <param name="operation" type="select" label="Operator">
9200 <option value="equal">equal</option>
9201 </param>
9202 <param name="value" type="select" label="Value">
9203 <option value="yes">yes</option>
9204 <option value="true">true</option>
9205 <option value="no">no</option>
9206 <option value="false">false</option>
9207 </param>
9208 </when>
9209 <when value="product">
9210 <param name="operation" type="select" label="Operator">
9211 <option value="equal">equal</option>
9212 <option value="different">different</option>
9213 </param>
9214 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9215 </when>
9216 <when value="description">
9217 <param name="operation" type="select" label="Operator">
9218 <option value="equal">equal</option>
9219 <option value="different">different</option>
9220 </param>
9221 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9222 </when>
9223 <when value="ecotype">
9224 <param name="operation" type="select" label="Operator">
9225 <option value="equal">equal</option>
9226 <option value="different">different</option>
9227 </param>
9228 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9229 </when>
9230 <when value="cell_type">
9231 <param name="operation" type="select" label="Operator">
9232 <option value="equal">equal</option>
9233 <option value="different">different</option>
9234 </param>
9235 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9236 </when>
9237 <when value="accession">
9238 <param name="operation" type="select" label="Operator">
9239 <option value="equal">equal</option>
9240 <option value="different">different</option>
9241 </param>
9242 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9243 </when>
9244 <when value="isolation_source">
9245 <param name="operation" type="select" label="Operator">
9246 <option value="equal">equal</option>
9247 <option value="different">different</option>
9248 </param>
9249 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9250 </when>
9251 <when value="mating_type">
9252 <param name="operation" type="select" label="Operator">
9253 <option value="equal">equal</option>
9254 <option value="different">different</option>
9255 </param>
9256 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9257 </when>
9258 <when value="tissue_type">
9259 <param name="operation" type="select" label="Operator">
9260 <option value="equal">equal</option>
9261 <option value="different">different</option>
9262 </param>
9263 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9264 </when>
9265 <when value="sub_strain">
9266 <param name="operation" type="select" label="Operator">
9267 <option value="equal">equal</option>
9268 <option value="different">different</option>
9269 </param>
9270 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9271 </when>
9272 <when value="tissue_lib">
9273 <param name="operation" type="select" label="Operator">
9274 <option value="equal">equal</option>
9275 <option value="different">different</option>
9276 </param>
9277 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9278 </when>
9279 <when value="cultivar">
9280 <param name="operation" type="select" label="Operator">
9281 <option value="equal">equal</option>
9282 <option value="different">different</option>
9283 </param>
9284 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9285 </when>
9286 <when value="base_count">
9287 <param name="operation" type="select" label="Operator">
9288 <option value="equal">equal</option>
9289 <option value="different">different</option>
9290 <option value="lower">lower</option>
9291 <option value="equal or lower">equal or lower</option>
9292 <option value="higher">higher</option>
9293 <option value="equal or higher">equal or higher</option>
9294 </param>
9295 <param name="value" type="float" value="" label="Any integer"/>
9296 </when>
9297 <when value="topology">
9298 <param name="operation" type="select" label="Operator">
9299 <option value="equal">equal</option>
9300 <option value="different">different</option>
9301 </param>
9302 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9303 </when>
9304 <when value="sub_species">
9305 <param name="operation" type="select" label="Operator">
9306 <option value="equal">equal</option>
9307 <option value="different">different</option>
9308 </param>
9309 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9310 </when>
9311 <when value="environmental_sample">
9312 <param name="operation" type="select" label="Operator">
9313 <option value="equal">equal</option>
9314 </param>
9315 <param name="value" type="select" label="Value">
9316 <option value="yes">yes</option>
9317 <option value="true">true</option>
9318 <option value="no">no</option>
9319 <option value="false">false</option>
9320 </param>
9321 </when>
9322 <when value="first_public">
9323 <param name="operation" type="select" label="Operator">
9324 <option value="equal">equal</option>
9325 <option value="different">different</option>
9326 <option value="lower">lower</option>
9327 <option value="equal or lower">equal or lower</option>
9328 <option value="higher">higher</option>
9329 <option value="equal or higher">equal or higher</option>
9330 </param>
9331 <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/>
9332 </when>
9333 <when value="strain">
9334 <param name="operation" type="select" label="Operator">
9335 <option value="equal">equal</option>
9336 <option value="different">different</option>
9337 </param>
9338 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9339 </when>
9340 <when value="country">
9341 <param name="operation" type="select" label="Operator">
9342 <option value="equal">equal</option>
9343 <option value="different">different</option>
9344 </param>
9345 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9346 </when>
9347 <when value="variety">
9348 <param name="operation" type="select" label="Operator">
9349 <option value="equal">equal</option>
9350 <option value="different">different</option>
9351 </param>
9352 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9353 </when>
9354 <when value="host">
9355 <param name="operation" type="select" label="Operator">
9356 <option value="equal">equal</option>
9357 <option value="different">different</option>
9358 </param>
9359 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9360 </when>
9361 <when value="gene_synonym">
9362 <param name="operation" type="select" label="Operator">
9363 <option value="equal">equal</option>
9364 <option value="different">different</option>
9365 </param>
9366 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9367 </when>
9368 <when value="organelle">
9369 <param name="operation" type="select" label="Operator">
9370 <option value="equal">equal</option>
9371 <option value="different">different</option>
9372 </param>
9373 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9374 </when>
9375 <when value="serovar">
9376 <param name="operation" type="select" label="Operator">
9377 <option value="equal">equal</option>
9378 <option value="different">different</option>
9379 </param>
9380 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9381 </when>
9382 <when value="rna_class">
9383 <param name="operation" type="select" label="Operator">
9384 <option value="equal">equal</option>
9385 <option value="different">different</option>
9386 </param>
9387 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9388 </when>
9389 <when value="dataclass">
9390 <param name="operation" type="select" label="Operator">
9391 <option value="equal">equal</option>
9392 <option value="different">different</option>
9393 </param>
9394 <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/>
9395 </when>
9396 <when value="gene">
9397 <param name="operation" type="select" label="Operator">
9398 <option value="equal">equal</option>
9399 <option value="different">different</option>
9400 </param>
9401 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9402 </when>
9403 <when value="culture_collection">
9404 <param name="operation" type="select" label="Operator">
9405 <option value="equal">equal</option>
9406 <option value="different">different</option>
9407 </param>
9408 <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/>
9409 </when>
9410 </conditional>
9411 </repeat>
9412 <conditional name="display_opt">
9413 <param argument="--display" type="select" label="Display option to specify the display format">
9414 <expand macro="display_options"/>
9415 </param>
9416 <when value="xml">
9417 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
9418 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
9419 </when>
9420 <when value="text">
9421 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
9422 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
9423 </when>
9424 <when value="fastq"/>
9425 <when value="html">
9426 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
9427 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
9428 </when>
9429 <when value="report">
9430 <param argument="--offset" type="integer" optional="true" label="First record to get"/>
9431 <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>
9432 <param argument="--fields" type="select" multiple="true" label="Fields to return">
9433 <option value="accession">accession</option>
9434 <option value="base_count">base_count</option>
9435 <option value="collected_by">collected_by</option>
9436 <option value="dataclass">dataclass</option>
9437 <option value="first_public">first_public</option>
9438 <option value="last_updated">last_updated</option>
9439 <option value="location">location</option>
9440 <option value="tax_division">tax_division</option>
9441 <option value="tax_id">tax_id</option>
9442 <option value="scientific_name">scientific_name</option>
9443 <option value="rna_class">rna_class</option>
9444 <option value="gene">gene</option>
9445 <option value="gene_synonym">gene_synonym</option>
9446 <option value="product">product</option>
9447 <option value="anticodon">anticodon</option>
9448 <option value="function">function</option>
9449 <option value="locus_tag">locus_tag</option>
9450 <option value="experiment">experiment</option>
9451 <option value="inference">inference</option>
9452 <option value="note">note</option>
9453 <option value="bio_material">bio_material</option>
9454 <option value="cell_line">cell_line</option>
9455 <option value="cell_type">cell_type</option>
9456 <option value="country">country</option>
9457 <option value="cultivar">cultivar</option>
9458 <option value="culture_collection">culture_collection</option>
9459 <option value="description">description</option>
9460 <option value="dev_stage">dev_stage</option>
9461 <option value="ecotype">ecotype</option>
9462 <option value="environmental_sample">environmental_sample</option>
9463 <option value="germline">germline</option>
9464 <option value="host">host</option>
9465 <option value="identified_by">identified_by</option>
9466 <option value="isolate">isolate</option>
9467 <option value="isolation_source">isolation_source</option>
9468 <option value="keywords">keywords</option>
9469 <option value="lab_host">lab_host</option>
9470 <option value="mating_type">mating_type</option>
9471 <option value="mol_type">mol_type</option>
9472 <option value="organelle">organelle</option>
9473 <option value="serotype">serotype</option>
9474 <option value="serovar">serovar</option>
9475 <option value="sex">sex</option>
9476 <option value="collection_date">collection_date</option>
9477 <option value="submitted_sex">submitted_sex</option>
9478 <option value="specimen_voucher">specimen_voucher</option>
9479 <option value="strain">strain</option>
9480 <option value="sub_species">sub_species</option>
9481 <option value="sub_strain">sub_strain</option>
9482 <option value="tissue_lib">tissue_lib</option>
9483 <option value="tissue_type">tissue_type</option>
9484 <option value="topology">topology</option>
9485 <option value="variety">variety</option>
9486 <option value="sequence_md5">sequence_md5</option>
9487 <option value="study_accession">study_accession</option>
9488 </param>
9489 <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">
9490 <option value="mol_type">in vivo molecule type of the sequence</option>
9491 <option value="last_updated">date when last updated</option>
9492 <option value="sequence_md5"></option>
9493 <option value="collected_by">name of the person who collected the specimen</option>
9494 <option value="serotype">serological variety of a species characterized by its antigenic properties</option>
9495 <option value="sex">sex of the organism from which the sample was obtained</option>
9496 <option value="keywords">keywords associated with sequence</option>
9497 <option value="cell_line">cell line from which the sample was obtained</option>
9498 <option value="inference">a structured description of non-experimental evidence</option>
9499 <option value="bio_material">identifier for biological material including institute and collection code</option>
9500 <option value="identified_by">name of the taxonomist who identified the specimen</option>
9501 <option value="note">any comment or additional information</option>
9502 <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option>
9503 <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option>
9504 <option value="tax_division">taxonomic division</option>
9505 <option value="collection_date">date that the specimen was collected</option>
9506 <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option>
9507 <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option>
9508 <option value="isolate">individual isolate from which sample was obtained</option>
9509 <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option>
9510 <option value="experiment">a brief description of the nature of the experimental evidence</option>
9511 <option value="location">geographic location of isolation of the sample</option>
9512 <option value="study_accession">study accession number</option>
9513 <option value="function">function attributed to a sequence</option>
9514 <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option>
9515 <option value="product">name of the product associated with the feature</option>
9516 <option value="description">brief sequence description</option>
9517 <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option>
9518 <option value="cell_type">cell type from which the sample was obtained</option>
9519 <option value="accession">accession number</option>
9520 <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option>
9521 <option value="mating_type">mating type of the organism from which the sequence was obtained</option>
9522 <option value="tissue_type">tissue type from which the sample was obtained</option>
9523 <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option>
9524 <option value="tissue_lib">tissue library from which sample was obtained</option>
9525 <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option>
9526 <option value="base_count">number of base pairs</option>
9527 <option value="topology">sequence topology: circular or linear</option>
9528 <option value="sub_species">name of sub-species of organism from which sample was obtained</option>
9529 <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option>
9530 <option value="first_public">date when made public</option>
9531 <option value="strain">strain from which sample was obtained</option>
9532 <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option>
9533 <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option>
9534 <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option>
9535 <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option>
9536 <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option>
9537 <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option>
9538 <option value="rna_class">classification of RNA</option>
9539 <option value="dataclass">sequence data class</option>
9540 <option value="gene">symbol of the gene corresponding to a sequence region</option>
9541 <option value="culture_collection">identifier for the sample culture including institute and collection code</option>
9542 </param>
9543 </when>
9544 <when value="fasta"/>
9545 </conditional>
9546 </when>
9547 </conditional>
9548 </xml>
9549 </macros>