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comparison ena_upload.xml @ 10:e7995727674f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
author iuc
date Mon, 27 Jan 2025 18:12:01 +0000
parents 69fc9c4a68b7
children fd7a4d3e07df
comparison
equal deleted inserted replaced
9:69fc9c4a68b7 10:e7995727674f
1 <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT"> 1 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT">
2 <description>Submission of (meta)data to the European Nucleotide Archive (ENA)</description>
2 <macros> 3 <macros>
3 <token name="@VERSION@">0.6.1</token> 4 <token name="@TOOL_VERSION@">0.7.5</token>
5 <token name="@VERSION_SUFFIX@">1</token>
4 <import>samples_macros.xml</import> 6 <import>samples_macros.xml</import>
5 </macros> 7 </macros>
6 <requirements> 8 <requirements>
7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement>
8 </requirements> 10 </requirements>
9 <stdio> 11 <stdio>
10 <regex match="Oops" source="stderr" level="fatal"/> 12 <regex match="Oops" source="stderr" level="fatal"/>
11 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/> 13 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
12 </stdio> 14 </stdio>
45 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path && 47 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
46 #end if 48 #end if
47 #if $action_options.input_format_conditional.input_format == "excel_tables": 49 #if $action_options.input_format_conditional.input_format == "excel_tables":
48 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx && 50 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
49 #end if 51 #end if
50 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False": 52 #if $action_options.input_format_conditional.input_format == "isa_json":
53 ln -s '$action_options.input_format_conditional.isa_json_file' ./isa_json_input.json &&
54 #end if
55 #if $action_options.test_submit_parameters.dry_run == "False":
51 webin_id=`grep 'username' $credentials`; 56 webin_id=`grep 'username' $credentials`;
52 if [ "\$webin_id" = "" ]; then 57 if [ "\$webin_id" = "" ]; then
53 ## No credentials in user defined preferences 58 ## No credentials in user defined preferences
54 ## Fallback to global defined credentials (if exist) 59 ## Fallback to global defined credentials (if exist)
55 #import os 60 #import os
56 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): 61 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
57 credentials_path=\${GALAXY_ENA_SECRETS}; 62 credentials_path=\${GALAXY_ENA_SECRETS};
58 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`; 63 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
59 if [ "\$webin_id" = "" ]; then 64 if [ "\$webin_id" = "" ]; then
60 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information"; 65 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
61 exit 1; 66 exit 1;
62 fi; 67 fi;
63 #else: 68 #else:
64 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information"; 69 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
65 exit 1; 70 exit 1;
78 #for $sample in $study.rep_sample: 83 #for $sample in $study.rep_sample:
79 #for $experiment in $sample.rep_experiment: 84 #for $experiment in $sample.rep_experiment:
80 #for $run in $experiment.rep_runs: 85 #for $run in $experiment.rep_runs:
81 #for $file in $run.upload_files: 86 #for $file in $run.upload_files:
82 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) 87 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
83 #if $action_options.input_format_conditional.add_extension == "true": 88 #if $action_options.input_format_conditional.add_extension == "True":
84 #set $extension = '.fastq' 89 #set $extension = '.fastq'
85 #else 90 #else
86 #set $extension = '' 91 #set $extension = ''
87 #end if 92 #end if
88 #if $file.is_of_type('fastq', 'fastqsanger'): 93 #if $file.is_of_type('fastq', 'fastqsanger'):
89 ## compression output is defined as safename_reads_file so no need to symlink 94 ## compression output is defined as safename_reads_file so no need to symlink
90 #set $safename_reads_file = $safename_reads_file + $extension + '.gz' 95 #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
91 gzip -c '$file' > $safename_reads_file && 96 gzip -c '$file' > $safename_reads_file &&
92 #else: 97 #else:
93 #if $action_options.input_format_conditional.add_extension == "true": 98 #if $action_options.input_format_conditional.add_extension == "True":
94 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): 99 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
95 #set $compression = '.gz' 100 #set $compression = '.gz'
96 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): 101 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
97 #set $compression = '.bz2' 102 #set $compression = '.bz2'
98 #end if 103 #end if
146 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list': 151 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
147 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data: 152 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
148 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) 153 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
149 #if $file.is_of_type('fastq', 'fastqsanger'): 154 #if $file.is_of_type('fastq', 'fastqsanger'):
150 ## always compress add the gz extension 155 ## always compress add the gz extension
151 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true": 156 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
152 #set $safename_reads_file = $safename_reads_file + '.fastq.gz' 157 #set $safename_reads_file = $safename_reads_file + '.fastq.gz'
153 #else 158 #else
154 #set $safename_reads_file = $safename_reads_file + '.gz' 159 #set $safename_reads_file = $safename_reads_file + '.gz'
155 #end if 160 #end if
156 gzip -c '$file' > $safename_reads_file && 161 gzip -c '$file' > $safename_reads_file &&
157 #else 162 #else
158 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true": 163 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
159 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): 164 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
160 #set $extension = '.fastq.gz' 165 #set $extension = '.fastq.gz'
161 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): 166 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
162 #set $extension = '.fastq.bz2' 167 #set $extension = '.fastq.bz2'
163 #end if 168 #end if
168 $files_to_upload.append(str($safename_reads_file)) 173 $files_to_upload.append(str($safename_reads_file))
169 #end for 174 #end for
170 #end if 175 #end if
171 #end if 176 #end if
172 177
173 #if $action_options.action == "add":
174 ena-upload-cli 178 ena-upload-cli
175 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' 179 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy'
176 --action '$action_options.action' 180 --action '$action_options.action'
177 --center '$action_options.center' 181 --center '$action_options.test_submit_parameters.center'
178 --secret \${credentials_path} 182 --secret \${credentials_path}
179 --data 183 --data
180 #for $dataset in $files_to_upload: 184 #for $dataset in $files_to_upload:
181 '$dataset' 185 '$dataset'
182 #end for 186 #end for
183 #if $action_options.test_submit_parameters.dry_run == "true": 187 #if $action_options.test_submit_parameters.dry_run == "True":
184 --draft 188 --draft
185 #end if 189 #end if
186 #if $action_options.input_format_conditional.input_format != "excel_tables": 190 #if $action_options.input_format_conditional.input_format == "excel_tables":
191 --xlsx ./xlsx_input.xlsx
192 #elif $action_options.input_format_conditional.input_format == "user_generated_tables" or $action_options.input_format_conditional.input_format == "build_tables":
187 --experiment '$experiments_table_path' 193 --experiment '$experiments_table_path'
188 --study '$studies_table_path' 194 --study '$studies_table_path'
189 --run '$runs_table_path' 195 --run '$runs_table_path'
190 --sample '$samples_table_path' 196 --sample '$samples_table_path'
191 #else 197 #elif $action_options.input_format_conditional.input_format == "isa_json":
192 --xlsx ./xlsx_input.xlsx 198 --isa_json ./isa_json_input.json
193 #end if 199 --isa_assay_stream '$action_options.input_format_conditional.isa_assay_stream'
194 --action add 200 #end if
195 #if $action_options.input_format_conditional.input_format == "user_generated_tables": 201 #if $action_options.input_format_conditional.input_format == "build_tables":
196 --checklist $action_options.input_format_conditional.checklist_id 202 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
203 --checklist ERC000033
204 #end if
205 #elif $action_options.input_format_conditional.input_format == "isa_json":
206 --checklist ERC000011
197 #else: 207 #else:
198 #if $action_options.input_format_conditional.input_format == "build_tables": 208 --checklist $action_options.input_format_conditional.checklist_id
199 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": 209 #end if
200 --checklist ERC000033 210 #if $action_options.test_submit_parameters.submit_dev == "True":
201 #end if
202 #else:
203 --checklist $action_options.input_format_conditional.checklist_id
204 #end if
205 #end if
206 #if $action_options.idempotent == "true":
207 --auto_action
208 #end if
209 #if $action_options.test_submit_parameters.submit_dev == "true":
210 -d 211 -d
211 #end if 212 #end if
212 >> '$output'; 213 >> '$output';
213 #end if 214
214 215
215 216 #if $action_options.test_submit_parameters.dry_run == "False":
216 217 echo -e 'center_name\t$action_options.test_submit_parameters.center' >> '$output';
217 #if $action_options.action == "modify":
218 ena-upload-cli
219 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
220 --action '$action_options.action'
221 --center '$action_options.center'
222 --secret \${credentials_path}
223 --data
224 #for $dataset in $files_to_upload:
225 '$dataset'
226 #end for
227 #if $action_options.test_submit_parameters.dry_run == "true":
228 --draft
229 #end if
230 #if $action_options.input_format_conditional.input_format != "excel_tables":
231 --experiment '$experiments_table_path'
232 --study '$studies_table_path'
233 --run '$runs_table_path'
234 --sample '$samples_table_path'
235 #else
236 --xlsx ./xlsx_input.xlsx
237 --auto_action
238 #end if
239 --action 'modify'
240 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
241 --checklist $action_options.input_format_conditional.checklist_id
242 #else:
243 #if $action_options.input_format_conditional.input_format == "build_tables":
244 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
245 --checklist ERC000033
246 #end if
247 #else:
248 --checklist $action_options.input_format_conditional.checklist_id
249 #end if
250 #end if
251 >> '$output';
252 #end if
253
254 #if $action_options.test_submit_parameters.dry_run == "false":
255 echo -e 'center_name\t$action_options.center' >> '$output';
256 echo -e 'action_option\t$action_options.action' >> '$output'; 218 echo -e 'action_option\t$action_options.action' >> '$output';
257 #end if 219 #end if
258 220
259 ## copy updated files 221 ## copy updated files
260 #if $action_options.input_format_conditional.input_format == "excel_tables": 222 #if $action_options.input_format_conditional.input_format == "excel_tables" or $action_options.input_format_conditional.input_format == "isa_json":
261 ## for the excel input case, copy the upload-cli generated tables to the output files 223 ## for the excel/ISA json input case, copy the upload-cli generated tables to the output files
262 ## this applies for both draft and real submissions 224 ## this applies for both draft and real submissions
263 cp './ENA_template_experiment_updated.tsv' $experiments_table_out; 225 cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
264 cp './ENA_template_sample_updated.tsv' $samples_table_out; 226 cp './ENA_template_sample_updated.tsv' $samples_table_out;
265 cp './ENA_template_study_updated.tsv' $studies_table_out; 227 cp './ENA_template_study_updated.tsv' $studies_table_out;
266 cp './ENA_template_run_updated.tsv' $runs_table_out; 228 cp './ENA_template_run_updated.tsv' $runs_table_out;
303 $runs.append((str($run.run_base_name),$run_files)) 265 $runs.append((str($run.run_base_name),$run_files))
304 #end for 266 #end for
305 267
306 $experiments.append({'title':str($experiment.experiment_title),'experiment_design':str($experiment.experiment_design),'library_strategy':str($experiment.library_strategy),'library_source':str($experiment.library_source),'library_selection':str($experiment.library_selection),'library_layout':str($experiment.library_layout),'insert_size':str($experiment.insert_size),'library_construction_protocol':str($experiment.library_construction_protocol),'platform':str($experiment.platform),'instrument_model':str($experiment.instrument_model),'runs':$runs}) 268 $experiments.append({'title':str($experiment.experiment_title),'experiment_design':str($experiment.experiment_design),'library_strategy':str($experiment.library_strategy),'library_source':str($experiment.library_source),'library_selection':str($experiment.library_selection),'library_layout':str($experiment.library_layout),'insert_size':str($experiment.insert_size),'library_construction_protocol':str($experiment.library_construction_protocol),'platform':str($experiment.platform),'instrument_model':str($experiment.instrument_model),'runs':$runs})
307 #end for 269 #end for
308 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": 270 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
309
310 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'host_common_name':str($sample.host_common_name),'host_subject_id':str($sample.host_subject_id),'host_health_state':str($sample.host_health_state),'host_sex':str($sample.host_sex),'host_scientific_name':str($sample.host_scientific_name),'collector_name':str($sample.collector_name),'collecting_institution':str($sample.collecting_institution),'isolate':str($sample.isolate),'experiments':$experiments}) 271 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'host_common_name':str($sample.host_common_name),'host_subject_id':str($sample.host_subject_id),'host_health_state':str($sample.host_health_state),'host_sex':str($sample.host_sex),'host_scientific_name':str($sample.host_scientific_name),'collector_name':str($sample.collector_name),'collecting_institution':str($sample.collecting_institution),'isolate':str($sample.isolate),'experiments':$experiments})
311 #else: 272 #else:
312 273 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'experiments':$experiments})
313 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'experiments':$experiments})
314 #end if 274 #end if
315 #end for 275 #end for
316 $studies.append({'title':str($study.study_title),'type':str($study.study_type),'abstract':str($study.study_abstract),'pubmed_id':str($study.study_pubmed_id),'samples':$samples}) 276 $studies.append({'title':str($study.study_title),'type':str($study.study_type),'abstract':str($study.study_abstract),'pubmed_id':str($study.study_pubmed_id),'samples':$samples})
317 #end for 277 #end for
318 #echo $json.dumps($studies) 278 #echo $json.dumps($studies)
320 </configfile> 280 </configfile>
321 </configfiles> 281 </configfiles>
322 <inputs> 282 <inputs>
323 <conditional name="action_options"> 283 <conditional name="action_options">
324 <param name="action" type="select" label="Action to execute"> 284 <param name="action" type="select" label="Action to execute">
325 <option value="add" selected="True">Add new data</option> 285 <option value="add" selected="True">Add new (meta)data</option>
326 <option value="modify">Modify metadata</option> 286 <option value="modify">Modify metadata</option>
327 </param> 287 </param>
328 <when value="add"> 288 <when value="add">
329 <param type="boolean" name="idempotent" checked="False" label="Idempotent submissions: only add the elements that were not submitted before" help="NOTE: this feature is based on a beta parameter of the CLI that checks the remote ENA repository for entries using the alias. This remote detection can have false positives, i.e assumes that it's present in the repository but it's not"/> 289 <param name="test_submit" type="hidden" value="False" />
330 <expand macro="test_submit_section"/> 290 <expand macro="table_inputs_macro" />
291 <expand macro="test_submit_section"/>
292 </when>
293 <when value="modify">
331 <param name="test_submit" type="hidden" value="False" /> 294 <param name="test_submit" type="hidden" value="False" />
332 <expand macro="table_inputs_macro" /> 295 <expand macro="table_inputs_macro" />
333 </when> 296 <expand macro="test_submit_section"/>
334 <when value="modify">
335 <expand macro="test_submit_section"/>
336 <param name="test_submit" type="hidden" value="False" />
337 <expand macro="table_inputs_macro" />
338 </when> 297 </when>
339 </conditional> 298 </conditional>
340 </inputs> 299 </inputs>
341 <outputs> 300 <outputs>
342 <data name="output" format="txt" label="ENA submission receipt"/> 301 <data name="output" format="txt" label="ENA submission receipt"/>
343 <data name="studies_table_out" format="tabular" label="Studies table"> 302 <data name="studies_table_out" format="tabular" label="Studies table">
344 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 303 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
345 </data> 304 </data>
346 <data name="samples_table_out" format="tabular" label="Samples table"> 305 <data name="samples_table_out" format="tabular" label="Samples table">
347 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 306 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
348 </data> 307 </data>
349 <data name="experiments_table_out" format="tabular" label="Experiments table"> 308 <data name="experiments_table_out" format="tabular" label="Experiments table">
350 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 309 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
351 </data> 310 </data>
352 <data name="runs_table_out" format="tabular" label="Runs table"> 311 <data name="runs_table_out" format="tabular" label="Runs table">
353 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 312 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
354 </data> 313 </data>
355 </outputs> 314 </outputs>
356 <tests> 315 <tests>
357 <!--Test 1: excel input of VIRAL samples --> 316 <!--Test 1: excel input of VIRAL samples -->
358 <test> 317 <test expect_num_outputs="5">
359 <conditional name="action_options"> 318 <conditional name="action_options">
360 <param name="action" value="add"/> 319 <param name="action" value="add"/>
361 <section name="test_submit_parameters"> 320 <section name="test_submit_parameters">
362 <param name="submit_dev" value="false" /> 321 <param name="center" value="Some research center"/>
363 <param name="dry_run" value="true" /> 322 <param name="submit_dev" value="False" />
323 <param name="dry_run" value="True" />
364 </section> 324 </section>
365 <conditional name="input_format_conditional"> 325 <conditional name="input_format_conditional">
366 <param name="input_format" value="excel_tables"/> 326 <param name="input_format" value="excel_tables"/>
367 <param name="checklist_id" value="ERC000033"/> 327 <param name="checklist_id" value="ERC000033"/>
368 <param name="xlsx_file" value="metadata_test_viral.xlsx"/> 328 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
369 <conditional name="run_input_format_conditional"> 329 <conditional name="run_input_format_conditional">
370 <param name="add_extension" value="false"/> 330 <param name="add_extension" value="False"/>
371 <param name="run_input_format" value="multiple_selection_list"/> 331 <param name="run_input_format" value="multiple_selection_list"/>
372 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/> 332 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
373 </conditional> 333 </conditional>
374 </conditional> 334 </conditional>
375 </conditional> 335 </conditional>
376 <param name="center" value="Some research center"/>
377 <output name="experiments_table_out"> 336 <output name="experiments_table_out">
378 <assert_contents> 337 <assert_contents>
379 <has_n_lines n="5"/> 338 <has_n_lines n="5"/>
380 <has_n_columns n="17"/> 339 <has_n_columns n="17"/>
381 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/> 340 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/>
397 </output> 356 </output>
398 <output name="runs_table_out"> 357 <output name="runs_table_out">
399 <assert_contents> 358 <assert_contents>
400 <has_n_lines n="5"/> 359 <has_n_lines n="5"/>
401 <has_n_columns n="8"/> 360 <has_n_columns n="8"/>
402 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> 361 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date\tstatus"/>
403 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> 362 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
404 </assert_contents> 363 </assert_contents>
405 </output> 364 </output>
406 </test> 365 </test>
407 <!--Test 2: excel input of VIRAL samples with extended columns--> 366 <!--Test 2: excel input of VIRAL samples with extended columns-->
408 <test> 367 <test expect_num_outputs="5">
409 <conditional name="action_options"> 368 <conditional name="action_options">
410 <param name="action" value="add"/> 369 <param name="action" value="add"/>
411 <section name="test_submit_parameters"> 370 <section name="test_submit_parameters">
412 <param name="submit_dev" value="false" /> 371 <param name="center" value="Some research center"/>
413 <param name="dry_run" value="true" /> 372 <param name="submit_dev" value="False" />
373 <param name="dry_run" value="True" />
414 </section> 374 </section>
415 <conditional name="input_format_conditional"> 375 <conditional name="input_format_conditional">
416 <param name="input_format" value="excel_tables"/> 376 <param name="input_format" value="excel_tables"/>
417 <param name="checklist_id" value="ERC000033"/> 377 <param name="checklist_id" value="ERC000033"/>
418 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/> 378 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
419 <conditional name="run_input_format_conditional"> 379 <conditional name="run_input_format_conditional">
420 <param name="add_extension" value="false"/> 380 <param name="add_extension" value="False"/>
421 <param name="run_input_format" value="multiple_selection_list"/> 381 <param name="run_input_format" value="multiple_selection_list"/>
422 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/> 382 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
423 </conditional> 383 </conditional>
424 </conditional> 384 </conditional>
425 </conditional> 385 </conditional>
426 <param name="center" value="Some research center"/>
427 <output name="experiments_table_out"> 386 <output name="experiments_table_out">
428 <assert_contents> 387 <assert_contents>
429 <has_n_lines n="5"/> 388 <has_n_lines n="5"/>
430 <has_n_columns n="17"/> 389 <has_n_columns n="17"/>
431 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/> 390 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/>
448 </output> 407 </output>
449 <output name="runs_table_out"> 408 <output name="runs_table_out">
450 <assert_contents> 409 <assert_contents>
451 <has_n_lines n="5"/> 410 <has_n_lines n="5"/>
452 <has_n_columns n="8"/> 411 <has_n_columns n="8"/>
453 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> 412 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date\tstatus"/>
454 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> 413 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
455 </assert_contents> 414 </assert_contents>
456 </output> 415 </output>
457 <output name="output"> 416 <output name="output">
458 <assert_contents> 417 <assert_contents>
463 <has_line_matching expression="ENA_run:"/> 422 <has_line_matching expression="ENA_run:"/>
464 </assert_contents> 423 </assert_contents>
465 </output> 424 </output>
466 </test> 425 </test>
467 <!--Test 3: excel input of NON-VIRAL samples--> 426 <!--Test 3: excel input of NON-VIRAL samples-->
468 <test> 427 <test expect_num_outputs="5">
469 <conditional name="action_options"> 428 <conditional name="action_options">
470 <param name="action" value="add"/> 429 <param name="action" value="add"/>
471 <section name="test_submit_parameters"> 430 <section name="test_submit_parameters">
472 <param name="submit_dev" value="false" /> 431 <param name="center" value="Some research center"/>
473 <param name="dry_run" value="true" /> 432 <param name="submit_dev" value="False" />
433 <param name="dry_run" value="True" />
474 </section> 434 </section>
475 <conditional name="input_format_conditional"> 435 <conditional name="input_format_conditional">
476 <param name="input_format" value="excel_tables"/> 436 <param name="input_format" value="excel_tables"/>
477 <param name="checklist_id" value="ERC000011"/> 437 <param name="checklist_id" value="ERC000011"/>
478 <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/> 438 <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/>
479 <conditional name="run_input_format_conditional"> 439 <conditional name="run_input_format_conditional">
480 <param name="add_extension" value="true"/> 440 <param name="add_extension" value="True"/>
481 <param name="run_input_format" value="multiple_selection_list"/> 441 <param name="run_input_format" value="multiple_selection_list"/>
482 <param name="data" value="sample_no_extension"/> 442 <param name="data" value="sample_no_extension"/>
483 </conditional> 443 </conditional>
484 </conditional> 444 </conditional>
485 </conditional> 445 </conditional>
486 <param name="center" value="Some research center"/>
487 <output name="experiments_table_out"> 446 <output name="experiments_table_out">
488 <assert_contents> 447 <assert_contents>
489 <has_n_lines n="2"/> 448 <has_n_lines n="2"/>
490 <has_n_columns n="17"/> 449 <has_n_columns n="17"/>
491 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/> 450 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/>
499 </assert_contents> 458 </assert_contents>
500 </output> 459 </output>
501 <output name="samples_table_out"> 460 <output name="samples_table_out">
502 <assert_contents> 461 <assert_contents>
503 <has_n_lines n="2"/> 462 <has_n_lines n="2"/>
463 <has_n_columns n="10"/>
464 <has_line_matching expression="s_20201007_026\tC026\tSaccharomyces cerevisiae\tSample from beer\t2020-03-25\tAntarctica\t\t\tADDED\t"/>
465 </assert_contents>
466 </output>
467 <output name="runs_table_out">
468 <assert_contents>
469 <has_n_lines n="2"/>
504 <has_n_columns n="8"/> 470 <has_n_columns n="8"/>
505 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/> 471 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date\tstatus"/>
506 </assert_contents>
507 </output>
508 <output name="runs_table_out">
509 <assert_contents>
510 <has_n_lines n="2"/>
511 <has_n_columns n="8"/>
512 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
513 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/> 472 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/>
514 </assert_contents> 473 </assert_contents>
515 </output> 474 </output>
516 </test> 475 </test>
517 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection --> 476 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
518 <test expect_failure="true"> 477 <test expect_failure="True">
519 <conditional name="action_options"> 478 <conditional name="action_options">
520 <param name="action" value="add"/> 479 <param name="action" value="add"/>
521 <section name="test_submit_parameters"> 480 <section name="test_submit_parameters">
522 <param name="submit_dev" value="false" /> 481 <param name="center" value="Some research center"/>
523 <param name="dry_run" value="false" /> 482 <param name="submit_dev" value="False" />
524 </section> 483 <param name="dry_run" value="False" />
525 <conditional name="input_format_conditional"> 484 </section>
526 <param name="add_extension" value="true"/> 485 <conditional name="input_format_conditional">
486 <param name="add_extension" value="True"/>
527 <param name="input_format" value="excel_tables"/> 487 <param name="input_format" value="excel_tables"/>
528 <param name="checklist_id" value="ERC000011"/> 488 <param name="checklist_id" value="ERC000011"/>
529 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> 489 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
530 <conditional name="run_input_format_conditional"> 490 <conditional name="run_input_format_conditional">
531 <param name="run_input_format" value="paired_list"/> 491 <param name="run_input_format" value="paired_list"/>
540 </collection> 500 </collection>
541 </param> 501 </param>
542 </conditional> 502 </conditional>
543 </conditional> 503 </conditional>
544 </conditional> 504 </conditional>
545 <param name="center" value="Some research center"/>
546 <assert_command> 505 <assert_command>
547 <has_text_matching expression="ena-upload-cli"/> 506 <has_text_matching expression="ena-upload-cli"/>
548 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/> 507 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
549 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 508 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
550 </assert_command> 509 </assert_command>
551 </test> 510 </test>
552 <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection + Idempotent submission --> 511 <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
553 <test expect_failure="true"> 512 <test expect_failure="True">
554 <conditional name="action_options"> 513 <conditional name="action_options">
555 <param name="action" value="add"/> 514 <param name="action" value="add"/>
556 <section name="test_submit_parameters"> 515 <section name="test_submit_parameters">
557 <param name="submit_dev" value="false" /> 516 <param name="center" value="Some research center"/>
558 <param name="dry_run" value="false" /> 517 <param name="submit_dev" value="False" />
559 </section> 518 <param name="dry_run" value="False" />
560 <param name="idempotent" value="true"/> 519 </section>
561 <conditional name="input_format_conditional"> 520 <conditional name="input_format_conditional">
562 <param name="add_extension" value="true"/> 521 <param name="add_extension" value="True"/>
563 <param name="input_format" value="excel_tables"/> 522 <param name="input_format" value="excel_tables"/>
564 <param name="checklist_id" value="ERC000011"/> 523 <param name="checklist_id" value="ERC000011"/>
565 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> 524 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
566 <conditional name="run_input_format_conditional"> 525 <conditional name="run_input_format_conditional">
567 <param name="run_input_format" value="paired_list"/> 526 <param name="run_input_format" value="paired_list"/>
576 </collection> 535 </collection>
577 </param> 536 </param>
578 </conditional> 537 </conditional>
579 </conditional> 538 </conditional>
580 </conditional> 539 </conditional>
581 <param name="center" value="Some research center"/>
582 <assert_command> 540 <assert_command>
583 <has_text_matching expression="ena-upload-cli"/> 541 <has_text_matching expression="ena-upload-cli"/>
584 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/> 542 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
585 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 543 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
586 <has_text_matching expression="--auto_action"/>
587 </assert_command> 544 </assert_command>
588 </test> 545 </test>
589 <!--Test 5: build tables from user input fields NON-VIRAL samples--> 546 <!--Test 5: build tables from user input fields NON-VIRAL samples-->
590 <test> 547 <test expect_num_outputs="5">
591 <conditional name="action_options"> 548 <conditional name="action_options">
592 <param name="action" value="add"/> 549 <param name="action" value="add"/>
593 <section name="test_submit_parameters"> 550 <section name="test_submit_parameters">
594 <param name="submit_dev" value="false" /> 551 <param name="center" value="Some research center"/>
595 <param name="dry_run" value="true" /> 552 <param name="submit_dev" value="False" />
553 <param name="dry_run" value="True" />
596 </section> 554 </section>
597 <conditional name="input_format_conditional"> 555 <conditional name="input_format_conditional">
598 <param name="input_format" value="build_tables"/> 556 <param name="input_format" value="build_tables"/>
599 <param name="add_extension" value="false"/> 557 <param name="add_extension" value="False"/>
600 <conditional name="conditional_viral_metadata"> 558 <conditional name="conditional_viral_metadata">
601 <param name="viral_sample" value="False"/> 559 <param name="viral_sample" value="False"/>
602 <repeat name="rep_study"> 560 <repeat name="rep_study">
603 <param name="study_title" value="Test study title"/> 561 <param name="study_title" value="Test study title"/>
604 <param name="study_abstract" value="Test study abstract"/> 562 <param name="study_abstract" value="Test study abstract"/>
607 <repeat name="rep_sample"> 565 <repeat name="rep_sample">
608 <param name="sample_title" value="Test Sample title"/> 566 <param name="sample_title" value="Test Sample title"/>
609 <param name="sample_description" value="Test Sample description"/> 567 <param name="sample_description" value="Test Sample description"/>
610 <param name="scientific_name" value="Test Sample scientific name"/> 568 <param name="scientific_name" value="Test Sample scientific name"/>
611 <param name="tax_id" value="2697049"/> 569 <param name="tax_id" value="2697049"/>
570 <param name="collection_date" value="2020"/>
571 <param name="geo_location_country" value="Belgium"/>
612 <repeat name="rep_experiment"> 572 <repeat name="rep_experiment">
613 <param name="experiment_title" value="Test experiment title"/> 573 <param name="experiment_title" value="Test experiment title"/>
614 <param name="experiment_design" value="Test experiment design description"/> 574 <param name="experiment_design" value="Test experiment design description"/>
615 <param name="library_strategy" value="CTS"/> 575 <param name="library_strategy" value="CTS"/>
616 <param name="library_source" value="GENOMIC"/> 576 <param name="library_source" value="GENOMIC"/>
627 </repeat> 587 </repeat>
628 </repeat> 588 </repeat>
629 </conditional> 589 </conditional>
630 </conditional> 590 </conditional>
631 </conditional> 591 </conditional>
632 <param name="center" value="Some research center"/>
633 <output name="experiments_table_out"> 592 <output name="experiments_table_out">
634 <assert_contents> 593 <assert_contents>
635 <has_n_lines n="2"/> 594 <has_n_lines n="2"/>
636 <has_n_columns n="17"/> 595 <has_n_columns n="17"/>
637 </assert_contents> 596 </assert_contents>
644 </assert_contents> 603 </assert_contents>
645 </output> 604 </output>
646 <output name="samples_table_out"> 605 <output name="samples_table_out">
647 <assert_contents> 606 <assert_contents>
648 <has_n_lines n="2"/> 607 <has_n_lines n="2"/>
649 <has_n_columns n="8"/> 608 <has_n_columns n="10"/>
650 </assert_contents> 609 </assert_contents>
651 </output> 610 </output>
652 <output name="runs_table_out"> 611 <output name="runs_table_out">
653 <assert_contents> 612 <assert_contents>
654 <has_n_lines n="3"/> 613 <has_n_lines n="3"/>
655 <has_n_columns n="8"/> 614 <has_n_columns n="8"/>
656 <has_line_matching expression="alias\tstatus\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tfile_checksum"/> 615 <has_line_matching expression="alias\tstatus\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date"/>
657 </assert_contents> 616 </assert_contents>
658 </output> 617 </output>
659 </test> 618 </test>
660 <!--Test 6: RUN failing build tables from user input fields NON-VIRAL samples--> 619 <!--Test 6: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
661 <test expect_failure="true"> 620 also tests compression of uncompressed inputs and adding the .gz suffix -->
621 <test expect_failure="False" expect_num_outputs="5">
662 <conditional name="action_options"> 622 <conditional name="action_options">
663 <param name="action" value="add"/> 623 <param name="action" value="add"/>
664 <section name="test_submit_parameters"> 624 <section name="test_submit_parameters">
665 <param name="submit_dev" value="true" /> 625 <param name="center" value="Some research center"/>
666 <param name="dry_run" value="false" /> 626 <param name="submit_dev" value="True" />
667 </section> 627 <param name="dry_run" value="True" />
668 <conditional name="input_format_conditional"> 628 </section>
629 <param name="test_submit" value="True"/>
630 <conditional name="input_format_conditional">
631 <param name="add_extension" value="False"/>
669 <param name="input_format" value="build_tables"/> 632 <param name="input_format" value="build_tables"/>
670 <param name="add_extension" value="true"/>
671 <conditional name="conditional_viral_metadata"> 633 <conditional name="conditional_viral_metadata">
672 <param name="viral_sample" value="false"/> 634 <param name="viral_sample" value="False"/>
673 <repeat name="rep_study"> 635 <repeat name="rep_study">
674 <param name="study_title" value="Test study title"/> 636 <param name="study_title" value="Test study title"/>
675 <param name="study_abstract" value="Test study abstract"/> 637 <param name="study_abstract" value="Test study abstract"/>
676 <param name="study_type" value="Epigenetics"/> 638 <param name="study_type" value="Epigenetics"/>
677 <param name="study_pubmed_id" value="Test study pubmedID"/> 639 <param name="study_pubmed_id" value="Test study pubmedID"/>
678 <repeat name="rep_sample"> 640 <repeat name="rep_sample">
679 <param name="sample_title" value="Test Sample title"/> 641 <param name="sample_title" value="Test Sample title"/>
680 <param name="sample_description" value="Test Sample description"/> 642 <param name="sample_description" value="Test Sample description"/>
681 <param name="scientific_name" value="Test Sample scientific name"/> 643 <param name="scientific_name" value="Test Sample scientific name"/>
682 <param name="tax_id" value="2697049"/> 644 <param name="tax_id" value="2697049"/>
683 <repeat name="rep_experiment"> 645 <param name="collection_date" value="2020"/>
684 <param name="experiment_title" value="Test experiment title"/> 646 <param name="geo_location_country" value="Belgium"/>
685 <param name="experiment_design" value="Test experiment design description"/>
686 <param name="library_strategy" value="CTS"/>
687 <param name="library_source" value="GENOMIC"/>
688 <param name="library_selection" value="PCR"/>
689 <param name="library_layout" value="SINGLE"/>
690 <param name="insert_size" value="150"/>
691 <param name="library_construction_protocol" value="Test library construction"/>
692 <param name="platform" value="ILLUMINA"/>
693 <param name="instrument_model" value="Illumina HiSeq 4000"/>
694 <repeat name="rep_runs">
695 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
696 </repeat>
697 </repeat>
698 </repeat>
699 </repeat>
700 </conditional>
701 </conditional>
702 </conditional>
703 <param name="center" value="Some research center"/>
704 <assert_stdout>
705 <has_text_matching expression="No ENA credentials defined"/>
706 </assert_stdout>
707 </test>
708 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
709 also tests compression of uncompressed inputs and adding the .gz suffix -->
710 <test expect_failure="false">
711 <conditional name="action_options">
712 <param name="action" value="add"/>
713 <section name="test_submit_parameters">
714 <param name="submit_dev" value="true" />
715 <param name="dry_run" value="true" />
716 </section>
717 <param name="test_submit" value="True"/>
718 <conditional name="input_format_conditional">
719 <param name="add_extension" value="false"/>
720 <param name="input_format" value="build_tables"/>
721 <conditional name="conditional_viral_metadata">
722 <param name="viral_sample" value="false"/>
723 <repeat name="rep_study">
724 <param name="study_title" value="Test study title"/>
725 <param name="study_abstract" value="Test study abstract"/>
726 <param name="study_type" value="Epigenetics"/>
727 <param name="study_pubmed_id" value="Test study pubmedID"/>
728 <repeat name="rep_sample">
729 <param name="sample_title" value="Test Sample title"/>
730 <param name="sample_description" value="Test Sample description"/>
731 <param name="scientific_name" value="Test Sample scientific name"/>
732 <param name="tax_id" value="2697049"/>
733 <repeat name="rep_experiment"> 647 <repeat name="rep_experiment">
734 <param name="experiment_title" value="Test experiment title"/> 648 <param name="experiment_title" value="Test experiment title"/>
735 <param name="experiment_design" value="Test experiment design description"/> 649 <param name="experiment_design" value="Test experiment design description"/>
736 <param name="library_strategy" value="CTS"/> 650 <param name="library_strategy" value="CTS"/>
737 <param name="library_source" value="GENOMIC"/> 651 <param name="library_source" value="GENOMIC"/>
749 </repeat> 663 </repeat>
750 </repeat> 664 </repeat>
751 </conditional> 665 </conditional>
752 </conditional> 666 </conditional>
753 </conditional> 667 </conditional>
754 <param name="center" value="Some research center"/>
755 <assert_command> 668 <assert_command>
756 <has_text_matching expression="ena-upload-cli"/> 669 <has_text_matching expression="ena-upload-cli"/>
757 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 670 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
758 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 671 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
759 <not_has_text text="modify" /> 672 <not_has_text text="modify" />
760 </assert_command> 673 </assert_command>
761 </test> 674 </test>
762 <!--Test 8: viral submission - User input metadata - Add extension = False--> 675 <!--Test 7: viral submission - User input metadata - Add extension = False-->
763 <test expect_failure="false"> 676 <test expect_failure="False" expect_num_outputs="5">
764 <conditional name="action_options"> 677 <conditional name="action_options">
765 <param name="action" value="add"/> 678 <param name="action" value="add"/>
766 <section name="test_submit_parameters"> 679 <section name="test_submit_parameters">
767 <param name="submit_dev" value="false" /> 680 <param name="center" value="Some research center"/>
768 <param name="dry_run" value="true" /> 681 <param name="submit_dev" value="False" />
682 <param name="dry_run" value="True" />
769 </section> 683 </section>
770 <param name="test_submit" value="True"/> 684 <param name="test_submit" value="True"/>
771 <conditional name="input_format_conditional"> 685 <conditional name="input_format_conditional">
772 <param name="add_extension" value="false"/> 686 <param name="add_extension" value="False"/>
773 <param name="input_format" value="build_tables"/> 687 <param name="input_format" value="build_tables"/>
774 <conditional name="conditional_viral_metadata"> 688 <conditional name="conditional_viral_metadata">
775 <param name="viral_sample" value="true"/> 689 <param name="viral_sample" value="True"/>
776 <repeat name="rep_study"> 690 <repeat name="rep_study">
777 <param name="study_title" value="Test study title"/> 691 <param name="study_title" value="Test study title"/>
778 <param name="study_abstract" value="Test study abstract"/> 692 <param name="study_abstract" value="Test study abstract"/>
779 <param name="study_type" value="Epigenetics"/> 693 <param name="study_type" value="Epigenetics"/>
780 <param name="study_pubmed_id" value="Test study pubmedID"/> 694 <param name="study_pubmed_id" value="Test study pubmedID"/>
812 </repeat> 726 </repeat>
813 </repeat> 727 </repeat>
814 </conditional> 728 </conditional>
815 </conditional> 729 </conditional>
816 </conditional> 730 </conditional>
817 <param name="center" value="Some research center"/>
818 <assert_command> 731 <assert_command>
819 <has_text_matching expression="ena-upload-cli"/> 732 <has_text_matching expression="ena-upload-cli"/>
820 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 733 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
821 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 734 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
822 <has_text_matching expression="--checklist ERC000033"/> 735 <has_text_matching expression="--checklist ERC000033"/>
823 </assert_command> 736 </assert_command>
824 </test> 737 </test>
825 <!--Test 9: modify option and auto compression - viral submission - User input metadata--> 738 <!--Test 8: modify option and auto compression - viral submission - User input metadata-->
826 <test expect_failure="false"> 739 <test expect_failure="False" expect_num_outputs="5">
827 <conditional name="action_options"> 740 <conditional name="action_options">
828 <param name="action" value="modify"/> 741 <param name="action" value="modify"/>
829 <section name="test_submit_parameters"> 742 <section name="test_submit_parameters">
830 <param name="submit_dev" value="false" /> 743 <param name="center" value="Some research center"/>
831 <param name="dry_run" value="true" /> 744 <param name="submit_dev" value="False" />
745 <param name="dry_run" value="True" />
832 </section> 746 </section>
833 <param name="test_submit" value="True"/> 747 <param name="test_submit" value="True"/>
834 <conditional name="input_format_conditional"> 748 <conditional name="input_format_conditional">
835 <param name="add_extension" value="fasle"/> 749 <param name="add_extension" value="False"/>
836 <param name="input_format" value="build_tables"/> 750 <param name="input_format" value="build_tables"/>
837 <conditional name="conditional_viral_metadata"> 751 <conditional name="conditional_viral_metadata">
838 <param name="viral_sample" value="True"/> 752 <param name="viral_sample" value="True"/>
839 <repeat name="rep_study"> 753 <repeat name="rep_study">
840 <param name="study_title" value="Test study title"/> 754 <param name="study_title" value="Test study title"/>
867 <param name="library_construction_protocol" value="Test library construction"/> 781 <param name="library_construction_protocol" value="Test library construction"/>
868 <param name="platform" value="ILLUMINA"/> 782 <param name="platform" value="ILLUMINA"/>
869 <param name="instrument_model" value="Illumina HiSeq 4000"/> 783 <param name="instrument_model" value="Illumina HiSeq 4000"/>
870 <repeat name="rep_runs"> 784 <repeat name="rep_runs">
871 <param name="run_base_name" value="run_from_hospital_X"/> 785 <param name="run_base_name" value="run_from_hospital_X"/>
872 <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/> 786 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
873 </repeat> 787 </repeat>
874 </repeat> 788 </repeat>
875 </repeat> 789 </repeat>
876 </repeat> 790 </repeat>
877 </conditional> 791 </conditional>
878 </conditional> 792 </conditional>
879 </conditional> 793 </conditional>
880 <param name="center" value="Some research center"/>
881 <assert_command> 794 <assert_command>
882 <has_text_matching expression="ena-upload-cli"/> 795 <has_text_matching expression="ena-upload-cli"/>
883 <has_text_matching expression="--data '1.fastqsanger.gz'"/> 796 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
884 <has_text_matching expression="--action 'modify' --center 'Some research center'"/> 797 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
885 <has_text_matching expression="--checklist ERC000033"/> 798 <has_text_matching expression="--checklist ERC000033"/>
886 <not_has_text text="add" /> 799 <not_has_text text="--action 'add'" />
887 </assert_command> 800 </assert_command>
888 </test> 801 </test>
802 <!--Test 9: isa JSON input of NON-VIRAL samples-->
803 <test expect_num_outputs="5">
804 <conditional name="action_options">
805 <param name="action" value="add"/>
806 <section name="test_submit_parameters">
807 <param name="center" value="Some research center"/>
808 <param name="submit_dev" value="True" />
809 <param name="dry_run" value="True" />
810 </section>
811 <conditional name="input_format_conditional">
812 <param name="input_format" value="isa_json"/>
813 <param name="isa_json_file" value="simple_test_case_v2.json"/>
814 <param name="isa_assay_stream" value="Ena stream 1"/>
815 <conditional name="run_input_format_conditional">
816 <param name="add_extension" value="False"/>
817 <param name="run_input_format" value="multiple_selection_list"/>
818 <param name="data" value="ENA_TEST1.R1.fastq.gz,ENA_TEST2.R1.fastq.gz,ENA_TEST2.R2.fastq.gz"/>
819 </conditional>
820 </conditional>
821 </conditional>
822 <output name="experiments_table_out">
823 <assert_contents>
824 <has_n_lines n="4"/>
825 <has_n_columns n="17"/>
826 <has_line_matching expression="alias\tstudy_alias\tsample_alias\tlibrary_name\ttitle\taccession\tsubmission date\tstatus\tdesign_description\tlibrary_source\tlibrary_strategy\tlibrary_selection\tlibrary_layout\tinsert_size\tplatform\tinstrument_model\tsubmission_date"/>
827 </assert_contents>
828 </output>
829 <output name="studies_table_out">
830 <assert_contents>
831 <has_n_lines n="2"/>
832 <has_n_columns n="9"/>
833 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\tnew_study_type\tpubmed_id\taccession\tsubmission_date\tstatus"/>
834 </assert_contents>
835 </output>
836 <output name="samples_table_out">
837 <assert_contents>
838 <has_n_lines n="3"/>
839 <has_n_columns n="11"/>
840 </assert_contents>
841 </output>
842 <output name="runs_table_out">
843 <assert_contents>
844 <has_n_lines n="4"/>
845 <has_n_columns n="10"/>
846 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_type\tfile checksum\taccession\tsubmission date\tstatus\tfile_checksum\tsubmission_date"/>
847 </assert_contents>
848 </output>
849 </test>
889 </tests> 850 </tests>
890 <help><![CDATA[ 851 <help><![CDATA[This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli. The input metadata can be submitted following the tabular format of the templates or their excel spreadsheet equivalent in https://github.com/ELIXIR-Belgium/ENA-metadata-templates. This template repo provides ready to use sheets for every ENA sample checklist and is automatically updated.
891 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli 852
892 The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables 853 .. class:: warningmark
893 It is also possible to submit an excel file by following the template in https://github.com/ELIXIR-Belgium/ENA-metadata-templates 854
894 ]]></help> 855 The ENA upload tool won't work unless you have provided an ENA Webin ID in User > Preferences > Manage Information > ENA Webin account details.]]></help>
895 <citations> 856 <citations>
857 <citation type="doi">doi:10.1093/bioinformatics/btab421</citation>
896 </citations> 858 </citations>
897 </tool> 859 </tool>