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comparison ena_upload.xml @ 7:6f6537780379 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
author iuc
date Thu, 24 Feb 2022 18:20:40 +0000
parents 4aab5ae907b6
children d147d6455873
comparison
equal deleted inserted replaced
6:4aab5ae907b6 7:6f6537780379
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="@VERSION@" profile="20.01" license="MIT">
2 <macros> 2 <macros>
3 <token name="@VERSION@">0.4.3</token> 3 <token name="@VERSION@">0.5.3</token>
4 <import>samples_macros.xml</import> 4 <import>samples_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement> 7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
8 <requirement type="package" version="1.2.0">xlrd</requirement>
9 </requirements> 8 </requirements>
10 <stdio> 9 <stdio>
11 <regex match="Oops" source="stderr" level="fatal"/> 10 <regex match="Oops" source="stderr" level="fatal"/>
12 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/> 11 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
13 </stdio> 12 </stdio>
25 24
26 #set working_dir = os.getcwd() 25 #set working_dir = os.getcwd()
27 #if $action_options.input_format_conditional.input_format == "build_tables": 26 #if $action_options.input_format_conditional.input_format == "build_tables":
28 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json; 27 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
29 #end if 28 #end if
30 29
31 #if $action_options.input_format_conditional.input_format == "excel_tables": 30 credentials_path='test_fake_path';
32 python '$__tool_directory__/process_xlsx.py' 31 echo "username: test_user" > \$credentials_path;
33 #if $action_options.input_format_conditional.viral_submission == "true": 32 echo "password: test_password" >> \$credentials_path;
34 --vir 33
35 #end if 34
36 #if $action_options.test_submit_parameters.submit_dev == "true": 35 #if $action_options.input_format_conditional.input_format == "build_tables":
37 --dev
38 #end if
39 --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files --verbose > '$output';
40 #end if
41
42 #if $action_options.input_format_conditional.input_format != "user_generated_tables":
43 cp $studies_table_path $studies_table_out && 36 cp $studies_table_path $studies_table_out &&
44 cp $samples_table_path $samples_table_out && 37 cp $samples_table_path $samples_table_out &&
45 cp $experiments_table_path $experiments_table_out && 38 cp $experiments_table_path $experiments_table_out &&
46 cp $runs_table_path $runs_table_out && 39 cp $runs_table_path $runs_table_out &&
47 #else: 40 #end if
41 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
48 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path && 42 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
49 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path && 43 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
50 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path && 44 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
51 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path && 45 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
52 #end if 46 #end if
53 47 #if $action_options.input_format_conditional.input_format == "excel_tables":
48 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
49 #end if
54 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False": 50 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
55 webin_id=`grep 'username' $credentials`; 51 webin_id=`grep 'username' $credentials`;
56 if [ "\$webin_id" = "" ]; then 52 if [ "\$webin_id" = "" ]; then
57 ## No credentials in user defined preferences 53 ## No credentials in user defined preferences
58 ## Fallback to global defined credentials (if exist) 54 ## Fallback to global defined credentials (if exist)
71 else 67 else
72 credentials_path='$credentials'; 68 credentials_path='$credentials';
73 fi; 69 fi;
74 #end if 70 #end if
75 71
76 #if $action_options.test_submit == "True":
77 credentials_path='test_fake_path';
78 #end if
79 72
80 ## create the list of files to upload and make the symlinks 73 ## create the list of files to upload and make the symlinks
81 #import re 74 #import re
82 #set $files_to_upload = list() 75 #set $files_to_upload = list()
83 #if $action_options.input_format_conditional.input_format == "build_tables": 76 #if $action_options.input_format_conditional.input_format == "build_tables":
154 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data: 147 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
155 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) 148 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
156 #if $file.is_of_type('fastq', 'fastqsanger'): 149 #if $file.is_of_type('fastq', 'fastqsanger'):
157 ## always compress add the gz extension 150 ## always compress add the gz extension
158 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true": 151 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
159 #set $safename_reads_file = $safename_reads_file + 'fastq.gz' 152 #set $safename_reads_file = $safename_reads_file + '.fastq.gz'
160 #else 153 #else
161 #set $safename_reads_file = $safename_reads_file + '.gz' 154 #set $safename_reads_file = $safename_reads_file + '.gz'
162 #end if 155 #end if
163 gzip -c '$file' > $safename_reads_file && 156 gzip -c '$file' > $safename_reads_file &&
164 #else 157 #else
165 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true": 158 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
166 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): 159 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
167 #set $extension = 'fastq.gz' 160 #set $extension = '.fastq.gz'
168 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): 161 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
169 #set $extension = 'fastq.bz2' 162 #set $extension = '.fastq.bz2'
170 #end if 163 #end if
171 #set $safename_reads_file = $safename_reads_file + $extension 164 #set $safename_reads_file = $safename_reads_file + $extension
172 #end if 165 #end if
173 ln -s '$file' $safename_reads_file && 166 ln -s '$file' $safename_reads_file &&
174 #end if 167 #end if
175 $files_to_upload.append(str($safename_reads_file)) 168 $files_to_upload.append(str($safename_reads_file))
176 #end for 169 #end for
177 #end if 170 #end if
178 #end if 171 #end if
179 172
180
181 #if $action_options.test_submit_parameters.dry_run == "false":
182 #if $action_options.action == "add": 173 #if $action_options.action == "add":
183 ena-upload-cli 174 ena-upload-cli
184 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' 175 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
185 --action '$action_options.action' 176 --action '$action_options.action'
186 --center '$action_options.center' 177 --center '$action_options.center'
187 --secret \${credentials_path} 178 --secret \${credentials_path}
188 --data 179 --data
189 #for $dataset in $files_to_upload: 180 #for $dataset in $files_to_upload:
190 '$dataset' 181 '$dataset'
191 #end for 182 #end for
183 #if $action_options.test_submit_parameters.dry_run == "true":
184 --draft
185 #end if
186 #if $action_options.input_format_conditional.input_format != "excel_tables":
187 --experiment '$experiments_table_path'
188 --study '$studies_table_path'
189 --run '$runs_table_path'
190 --sample '$samples_table_path'
191 #else
192 --xlsx ./xlsx_input.xlsx
193 #end if
192 --action add 194 --action add
193 --experiment '$experiments_table_path'
194 --study '$studies_table_path'
195 --run '$runs_table_path'
196 --sample '$samples_table_path'
197 #if $action_options.input_format_conditional.input_format == "user_generated_tables": 195 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
198 #if "$action_options.input_format_conditional.viral_submission" == "true": 196 --checklist $action_options.input_format_conditional.checklist_id
199 --checklist ERC000033
200 #end if
201 #else: 197 #else:
202 #if $action_options.input_format_conditional.input_format == "build_tables": 198 #if $action_options.input_format_conditional.input_format == "build_tables":
203 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": 199 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
204 --checklist ERC000033 200 --checklist ERC000033
205 #end if 201 #end if
206 #else: 202 #else:
207 #if $action_options.input_format_conditional.viral_submission == "true": 203 --checklist $action_options.input_format_conditional.checklist_id
208 --checklist ERC000033
209 #end if
210 #end if 204 #end if
211 #end if 205 #end if
212 206
213 #if $action_options.test_submit_parameters.submit_dev == "true": 207 #if $action_options.test_submit_parameters.submit_dev == "true":
214 -d 208 -d
215 #end if 209 #end if
216 >> '$output'; 210 >> '$output';
217 #end if 211 #end if
212
213
218 214
219 #if $action_options.action == "modify": 215 #if $action_options.action == "modify":
220 ena-upload-cli 216 ena-upload-cli
221 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' 217 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
222 --action '$action_options.action' 218 --action '$action_options.action'
224 --secret \${credentials_path} 220 --secret \${credentials_path}
225 --data 221 --data
226 #for $dataset in $files_to_upload: 222 #for $dataset in $files_to_upload:
227 '$dataset' 223 '$dataset'
228 #end for 224 #end for
225 #if $action_options.test_submit_parameters.dry_run == "true":
226 --draft
227 #end if
228 #if $action_options.input_format_conditional.input_format != "excel_tables":
229 --experiment '$experiments_table_path'
230 --study '$studies_table_path'
231 --run '$runs_table_path'
232 --sample '$samples_table_path'
233 #else
234 --xlsx ./xlsx_input.xlsx
235 --auto_action
236 #end if
229 --action 'modify' 237 --action 'modify'
230 --experiment '$experiments_table_path'
231 --study '$studies_table_path'
232 --run '$runs_table_path'
233 --sample '$samples_table_path'
234 #if $action_options.input_format_conditional.input_format == "user_generated_tables": 238 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
235 #if "$action_options.input_format_conditional.viral_submission" == "true": 239 --checklist $action_options.input_format_conditional.checklist_id
236 --checklist ERC000033
237 #end if
238 #else: 240 #else:
239 #if $action_options.input_format_conditional.input_format == "build_tables": 241 #if $action_options.input_format_conditional.input_format == "build_tables":
240 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": 242 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
241 --checklist ERC000033 243 --checklist ERC000033
242 #end if 244 #end if
243 #else: 245 #else:
244 #if $action_options.input_format_conditional.viral_submission == "true": 246 --checklist $action_options.input_format_conditional.checklist_id
245 --checklist ERC000033
246 #end if
247 #end if 247 #end if
248 #end if 248 #end if
249 >> '$output'; 249 >> '$output';
250 #end if 250 #end if
251
252 #if $action_options.test_submit_parameters.dry_run == "false":
251 echo -e 'center_name\t$action_options.center' >> '$output'; 253 echo -e 'center_name\t$action_options.center' >> '$output';
252 echo -e 'action_option\t$action_options.action' >> '$output'; 254 echo -e 'action_option\t$action_options.action' >> '$output';
253 #if $action_options.input_format_conditional.input_format != "user_generated_tables": 255 #end if
254 cp $studies_table_path_updated $studies_table_out 2>/dev/null; 256
255 cp $samples_table_path_updated $samples_table_out 2>/dev/null; 257 ## copy updated files
256 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null; 258 #if $action_options.input_format_conditional.input_format == "excel_tables":
257 cp $runs_table_path_updated $runs_table_out 2>/dev/null; 259 ## for the excel input case, copy the upload-cli generated tables to the output files
258 #end if 260 ## this applies for both draft and real submissions
259 #else: 261 cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
260 exit 0; 262 cp './ENA_template_sample_updated.tsv' $samples_table_out;
261 #end if 263 cp './ENA_template_study_updated.tsv' $studies_table_out;
262 264 cp './ENA_template_run_updated.tsv' $runs_table_out;
265 #else
266 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
267 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
268 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
269 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
270 #end if
271
272 python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output;
263 ]]></command> 273 ]]></command>
264 <configfiles> 274 <configfiles>
265 <configfile name="credentials"><![CDATA[ 275 <configfile name="credentials"><![CDATA[
266 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip() 276 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
267 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip() 277 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
339 <data name="runs_table_out" format="tabular" label="Runs table"> 349 <data name="runs_table_out" format="tabular" label="Runs table">
340 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 350 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
341 </data> 351 </data>
342 </outputs> 352 </outputs>
343 <tests> 353 <tests>
344 <!--Test 1: excel input of VIRAL samples --> 354 <!--Test 1: excel input of VIRAL samples -->
345 <test> 355 <test>
346 <conditional name="action_options"> 356 <conditional name="action_options">
347 <param name="action" value="add"/> 357 <param name="action" value="add"/>
348 <section name="test_submit_parameters"> 358 <section name="test_submit_parameters">
349 <param name="submit_dev" value="false" /> 359 <param name="submit_dev" value="false" />
350 <param name="dry_run" value="true" /> 360 <param name="dry_run" value="true" />
351 </section> 361 </section>
352 <conditional name="input_format_conditional"> 362 <conditional name="input_format_conditional">
353 <param name="input_format" value="excel_tables"/> 363 <param name="input_format" value="excel_tables"/>
354 <param name="viral_submission" value="True"/> 364 <param name="checklist_id" value="ERC000033"/>
355 <param name="xlsx_file" value="metadata_test_viral.xlsx"/> 365 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
356 <conditional name="run_input_format_conditional"> 366 <conditional name="run_input_format_conditional">
357 <param name="add_extension" value="true"/> 367 <param name="add_extension" value="false"/>
358 <param name="run_input_format" value="multiple_selection_list"/> 368 <param name="run_input_format" value="multiple_selection_list"/>
359 <param name="data" value="sample.fq"/> 369 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
360 </conditional> 370 </conditional>
361 </conditional> 371 </conditional>
362 </conditional> 372 </conditional>
363 <param name="center" value="Some research center"/> 373 <param name="center" value="Some research center"/>
364 <output name="experiments_table_out"> 374 <output name="experiments_table_out">
365 <assert_contents> 375 <assert_contents>
366 <has_n_lines n="5"/> 376 <has_n_lines n="5"/>
367 <has_n_columns n="17"/> 377 <has_n_columns n="17"/>
368 <has_line_matching expression="alias\tstatus\taccession\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\tsubmission_date" /> 378 <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"/>
369 <has_line_matching expression="e_(.*)_026\tmodify\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> 379 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
370 </assert_contents> 380 </assert_contents>
371 </output> 381 </output>
372 <output name="studies_table_out"> 382 <output name="studies_table_out">
373 <assert_contents> 383 <assert_contents>
374 <has_n_lines n="2"/> 384 <has_n_lines n="2"/>
375 <has_n_columns n="8"/> 385 <has_n_columns n="7"/>
376 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> 386 <has_line_matching expression="SARS-CoV-2_genomes_01\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/>
377 <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/>
378 </assert_contents> 387 </assert_contents>
379 </output> 388 </output>
380 <output name="samples_table_out"> 389 <output name="samples_table_out">
381 <assert_contents> 390 <assert_contents>
382 <has_n_lines n="5"/> 391 <has_n_lines n="5"/>
385 </output> 394 </output>
386 <output name="runs_table_out"> 395 <output name="runs_table_out">
387 <assert_contents> 396 <assert_contents>
388 <has_n_lines n="5"/> 397 <has_n_lines n="5"/>
389 <has_n_columns n="8"/> 398 <has_n_columns n="8"/>
390 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/> 399 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
391 <has_line_matching expression="r_(.*)_026\tmodify\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\t\tsubmission_date_ENA"/> 400 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
392 </assert_contents> 401 </assert_contents>
393 </output> 402 </output>
394 </test> 403 </test>
395 <!--Test 2: excel input of VIRAL samples with extended columns--> 404 <!--Test 2: excel input of VIRAL samples with extended columns-->
396 <test> 405 <test>
400 <param name="submit_dev" value="false" /> 409 <param name="submit_dev" value="false" />
401 <param name="dry_run" value="true" /> 410 <param name="dry_run" value="true" />
402 </section> 411 </section>
403 <conditional name="input_format_conditional"> 412 <conditional name="input_format_conditional">
404 <param name="input_format" value="excel_tables"/> 413 <param name="input_format" value="excel_tables"/>
405 <param name="viral_submission" value="True"/> 414 <param name="checklist_id" value="ERC000033"/>
406 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/> 415 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
407 <conditional name="run_input_format_conditional"> 416 <conditional name="run_input_format_conditional">
408 <param name="add_extension" value="true"/> 417 <param name="add_extension" value="false"/>
409 <param name="run_input_format" value="multiple_selection_list"/> 418 <param name="run_input_format" value="multiple_selection_list"/>
410 <param name="data" value="sample.fq"/> 419 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
411 </conditional> 420 </conditional>
412 </conditional> 421 </conditional>
413 </conditional> 422 </conditional>
414 <param name="center" value="Some research center"/> 423 <param name="center" value="Some research center"/>
415 <output name="experiments_table_out"> 424 <output name="experiments_table_out">
416 <assert_contents> 425 <assert_contents>
417 <has_n_lines n="5"/> 426 <has_n_lines n="5"/>
418 <has_n_columns n="17"/> 427 <has_n_columns n="17"/>
419 <has_line_matching expression="alias\tstatus\taccession\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\tsubmission_date" /> 428 <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"/>
420 <has_line_matching expression="e_(.*)_026\tmodify\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> 429 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
421 </assert_contents> 430 </assert_contents>
422 </output> 431 </output>
423 <output name="studies_table_out"> 432 <output name="studies_table_out">
424 <assert_contents> 433 <assert_contents>
425 <has_n_lines n="2"/> 434 <has_n_lines n="2"/>
426 <has_n_columns n="8"/> 435 <has_n_columns n="7"/>
427 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> 436 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/>
428 <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> 437 <has_line_matching expression="SARS-CoV-2_genomes_01\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/>
429 </assert_contents> 438 </assert_contents>
430 </output> 439 </output>
431 <output name="samples_table_out"> 440 <output name="samples_table_out">
432 <assert_contents> 441 <assert_contents>
433 <has_n_lines n="5"/> 442 <has_n_lines n="5"/>
434 <has_n_columns n="42"/> 443 <has_n_columns n="43"/>
435 </assert_contents> 444 </assert_contents>
436 </output> 445 </output>
437 <output name="runs_table_out"> 446 <output name="runs_table_out">
438 <assert_contents> 447 <assert_contents>
439 <has_n_lines n="5"/> 448 <has_n_lines n="5"/>
440 <has_n_columns n="8"/> 449 <has_n_columns n="8"/>
441 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/> 450 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
442 <has_line_matching expression="r_(.*)_026\tmodify\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\t\tsubmission_date_ENA"/> 451 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
452 </assert_contents>
453 </output>
454 <output name="output">
455 <assert_contents>
456 <has_line_matching expression="YAML -------------"/>
457 <has_line_matching expression="ENA_experiment:"/>
458 <has_line_matching expression="ENA_sample:"/>
459 <has_line_matching expression="ENA_study:"/>
460 <has_line_matching expression="ENA_run:"/>
443 </assert_contents> 461 </assert_contents>
444 </output> 462 </output>
445 </test> 463 </test>
446 <!--Test 3: excel input of NON-VIRAL samples--> 464 <!--Test 3: excel input of NON-VIRAL samples-->
447 <test> 465 <test>
451 <param name="submit_dev" value="false" /> 469 <param name="submit_dev" value="false" />
452 <param name="dry_run" value="true" /> 470 <param name="dry_run" value="true" />
453 </section> 471 </section>
454 <conditional name="input_format_conditional"> 472 <conditional name="input_format_conditional">
455 <param name="input_format" value="excel_tables"/> 473 <param name="input_format" value="excel_tables"/>
456 <param name="viral_submission" value="False"/> 474 <param name="checklist_id" value="ERC000011"/>
457 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> 475 <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/>
458 <conditional name="run_input_format_conditional"> 476 <conditional name="run_input_format_conditional">
459 <param name="add_extension" value="true"/> 477 <param name="add_extension" value="true"/>
460 <param name="run_input_format" value="multiple_selection_list"/> 478 <param name="run_input_format" value="multiple_selection_list"/>
461 <param name="data" value="sample.fq"/> 479 <param name="data" value="sample_no_extension"/>
462 </conditional> 480 </conditional>
463 </conditional> 481 </conditional>
464 </conditional> 482 </conditional>
465 <param name="center" value="Some research center"/> 483 <param name="center" value="Some research center"/>
466 <output name="experiments_table_out"> 484 <output name="experiments_table_out">
467 <assert_contents> 485 <assert_contents>
468 <has_n_lines n="5"/> 486 <has_n_lines n="2"/>
469 <has_n_columns n="17"/> 487 <has_n_columns n="17"/>
470 <has_line_matching expression="alias\tstatus\taccession\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\tsubmission_date" /> 488 <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"/>
471 </assert_contents> 489 </assert_contents>
472 </output> 490 </output>
473 <output name="studies_table_out"> 491 <output name="studies_table_out">
492 <assert_contents>
493 <has_n_lines n="2"/>
494 <has_n_columns n="7"/>
495 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/>
496 </assert_contents>
497 </output>
498 <output name="samples_table_out">
474 <assert_contents> 499 <assert_contents>
475 <has_n_lines n="2"/> 500 <has_n_lines n="2"/>
476 <has_n_columns n="8"/> 501 <has_n_columns n="8"/>
477 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> 502 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/>
478 </assert_contents> 503 </assert_contents>
479 </output> 504 </output>
480 <output name="samples_table_out"> 505 <output name="runs_table_out">
481 <assert_contents> 506 <assert_contents>
482 <has_n_lines n="5"/> 507 <has_n_lines n="2"/>
483 <has_n_columns n="8"/> 508 <has_n_columns n="8"/>
484 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date"/> 509 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
485 </assert_contents> 510 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/>
486 </output>
487 <output name="runs_table_out">
488 <assert_contents>
489 <has_n_lines n="5"/>
490 <has_n_columns n="8"/>
491 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
492 <has_line_matching expression="r_(.*)_026\tmodify\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\t\tsubmission_date_ENA"/>
493 </assert_contents> 511 </assert_contents>
494 </output> 512 </output>
495 </test> 513 </test>
496 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection --> 514 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
497 <test expect_failure="true"> 515 <test expect_failure="true">
502 <param name="dry_run" value="false" /> 520 <param name="dry_run" value="false" />
503 </section> 521 </section>
504 <conditional name="input_format_conditional"> 522 <conditional name="input_format_conditional">
505 <param name="add_extension" value="true"/> 523 <param name="add_extension" value="true"/>
506 <param name="input_format" value="excel_tables"/> 524 <param name="input_format" value="excel_tables"/>
507 <param name="viral_submission" value="False"/> 525 <param name="checklist_id" value="ERC000011"/>
508 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> 526 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
509 <conditional name="run_input_format_conditional"> 527 <conditional name="run_input_format_conditional">
510 <param name="run_input_format" value="paired_list"/> 528 <param name="run_input_format" value="paired_list"/>
511 <param name="paired_end_collection"> 529 <param name="paired_end_collection">
512 <collection type="list:paired"> 530 <collection type="list:paired">
536 <param name="submit_dev" value="false" /> 554 <param name="submit_dev" value="false" />
537 <param name="dry_run" value="true" /> 555 <param name="dry_run" value="true" />
538 </section> 556 </section>
539 <conditional name="input_format_conditional"> 557 <conditional name="input_format_conditional">
540 <param name="input_format" value="build_tables"/> 558 <param name="input_format" value="build_tables"/>
541 <param name="add_extension" value="true"/> 559 <param name="add_extension" value="false"/>
542 <conditional name="conditional_viral_metadata"> 560 <conditional name="conditional_viral_metadata">
543 <param name="viral_sample" value="False"/> 561 <param name="viral_sample" value="False"/>
544 <repeat name="rep_study"> 562 <repeat name="rep_study">
545 <param name="study_title" value="Test study title"/> 563 <param name="study_title" value="Test study title"/>
546 <param name="study_abstract" value="Test study abstract"/> 564 <param name="study_abstract" value="Test study abstract"/>
548 <param name="study_pubmed_id" value="Test study pubmedID"/> 566 <param name="study_pubmed_id" value="Test study pubmedID"/>
549 <repeat name="rep_sample"> 567 <repeat name="rep_sample">
550 <param name="sample_title" value="Test Sample title"/> 568 <param name="sample_title" value="Test Sample title"/>
551 <param name="sample_description" value="Test Sample description"/> 569 <param name="sample_description" value="Test Sample description"/>
552 <param name="scientific_name" value="Test Sample scientific name"/> 570 <param name="scientific_name" value="Test Sample scientific name"/>
553 <param name="tax_id" value="Test Sample tax_id"/> 571 <param name="tax_id" value="2697049"/>
554 <repeat name="rep_experiment"> 572 <repeat name="rep_experiment">
555 <param name="experiment_title" value="Test experiment title"/> 573 <param name="experiment_title" value="Test experiment title"/>
556 <param name="experiment_design" value="Test experiment design description"/> 574 <param name="experiment_design" value="Test experiment design description"/>
557 <param name="library_strategy" value="CTS"/> 575 <param name="library_strategy" value="CTS"/>
558 <param name="library_source" value="GENOMIC"/> 576 <param name="library_source" value="GENOMIC"/>
561 <param name="insert_size" value="150"/> 579 <param name="insert_size" value="150"/>
562 <param name="library_construction_protocol" value="Test library construction"/> 580 <param name="library_construction_protocol" value="Test library construction"/>
563 <param name="platform" value="ILLUMINA"/> 581 <param name="platform" value="ILLUMINA"/>
564 <param name="instrument_model" value="Illumina HiSeq 4000"/> 582 <param name="instrument_model" value="Illumina HiSeq 4000"/>
565 <repeat name="rep_runs"> 583 <repeat name="rep_runs">
566 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> 584 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger.gz"/>
567 </repeat> 585 </repeat>
568 </repeat> 586 </repeat>
569 </repeat> 587 </repeat>
570 </repeat> 588 </repeat>
571 </conditional> 589 </conditional>
619 <param name="study_pubmed_id" value="Test study pubmedID"/> 637 <param name="study_pubmed_id" value="Test study pubmedID"/>
620 <repeat name="rep_sample"> 638 <repeat name="rep_sample">
621 <param name="sample_title" value="Test Sample title"/> 639 <param name="sample_title" value="Test Sample title"/>
622 <param name="sample_description" value="Test Sample description"/> 640 <param name="sample_description" value="Test Sample description"/>
623 <param name="scientific_name" value="Test Sample scientific name"/> 641 <param name="scientific_name" value="Test Sample scientific name"/>
624 <param name="tax_id" value="Test Sample tax_id"/> 642 <param name="tax_id" value="2697049"/>
625 <repeat name="rep_experiment"> 643 <repeat name="rep_experiment">
626 <param name="experiment_title" value="Test experiment title"/> 644 <param name="experiment_title" value="Test experiment title"/>
627 <param name="experiment_design" value="Test experiment design description"/> 645 <param name="experiment_design" value="Test experiment design description"/>
628 <param name="library_strategy" value="CTS"/> 646 <param name="library_strategy" value="CTS"/>
629 <param name="library_source" value="GENOMIC"/> 647 <param name="library_source" value="GENOMIC"/>
647 <has_text_matching expression="No ENA credentials defined"/> 665 <has_text_matching expression="No ENA credentials defined"/>
648 </assert_stdout> 666 </assert_stdout>
649 </test> 667 </test>
650 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples 668 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
651 also tests compression of uncompressed inputs and adding the .gz suffix --> 669 also tests compression of uncompressed inputs and adding the .gz suffix -->
652 <test expect_failure="true"> 670 <test expect_failure="false">
653 <conditional name="action_options"> 671 <conditional name="action_options">
654 <param name="action" value="add"/> 672 <param name="action" value="add"/>
655 <section name="test_submit_parameters"> 673 <section name="test_submit_parameters">
656 <param name="submit_dev" value="true" /> 674 <param name="submit_dev" value="true" />
657 <param name="dry_run" value="false" /> 675 <param name="dry_run" value="true" />
658 </section> 676 </section>
659 <param name="test_submit" value="True"/> 677 <param name="test_submit" value="True"/>
660 <conditional name="input_format_conditional"> 678 <conditional name="input_format_conditional">
661 <param name="add_extension" value="true"/> 679 <param name="add_extension" value="false"/>
662 <param name="input_format" value="build_tables"/> 680 <param name="input_format" value="build_tables"/>
663 <conditional name="conditional_viral_metadata"> 681 <conditional name="conditional_viral_metadata">
664 <param name="viral_sample" value="false"/> 682 <param name="viral_sample" value="false"/>
665 <repeat name="rep_study"> 683 <repeat name="rep_study">
666 <param name="study_title" value="Test study title"/> 684 <param name="study_title" value="Test study title"/>
669 <param name="study_pubmed_id" value="Test study pubmedID"/> 687 <param name="study_pubmed_id" value="Test study pubmedID"/>
670 <repeat name="rep_sample"> 688 <repeat name="rep_sample">
671 <param name="sample_title" value="Test Sample title"/> 689 <param name="sample_title" value="Test Sample title"/>
672 <param name="sample_description" value="Test Sample description"/> 690 <param name="sample_description" value="Test Sample description"/>
673 <param name="scientific_name" value="Test Sample scientific name"/> 691 <param name="scientific_name" value="Test Sample scientific name"/>
674 <param name="tax_id" value="Test Sample tax_id"/> 692 <param name="tax_id" value="2697049"/>
675 <repeat name="rep_experiment"> 693 <repeat name="rep_experiment">
676 <param name="experiment_title" value="Test experiment title"/> 694 <param name="experiment_title" value="Test experiment title"/>
677 <param name="experiment_design" value="Test experiment design description"/> 695 <param name="experiment_design" value="Test experiment design description"/>
678 <param name="library_strategy" value="CTS"/> 696 <param name="library_strategy" value="CTS"/>
679 <param name="library_source" value="GENOMIC"/> 697 <param name="library_source" value="GENOMIC"/>
683 <param name="library_construction_protocol" value="Test library construction"/> 701 <param name="library_construction_protocol" value="Test library construction"/>
684 <param name="platform" value="ILLUMINA"/> 702 <param name="platform" value="ILLUMINA"/>
685 <param name="instrument_model" value="Illumina HiSeq 4000"/> 703 <param name="instrument_model" value="Illumina HiSeq 4000"/>
686 <repeat name="rep_runs"> 704 <repeat name="rep_runs">
687 <param name="run_base_name" value="run_from_hospital_X"/> 705 <param name="run_base_name" value="run_from_hospital_X"/>
688 <param name="upload_files" value="sample.fq,sample.fq" ftype="fastqsanger"/> 706 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
689 </repeat> 707 </repeat>
690 </repeat> 708 </repeat>
691 </repeat> 709 </repeat>
692 </repeat> 710 </repeat>
693 </conditional> 711 </conditional>
694 </conditional> 712 </conditional>
695 </conditional> 713 </conditional>
696 <param name="center" value="Some research center"/> 714 <param name="center" value="Some research center"/>
697 <assert_command> 715 <assert_command>
698 <has_text_matching expression="ena-upload-cli"/> 716 <has_text_matching expression="ena-upload-cli"/>
699 <has_text_matching expression="--data 'sample.fq.fastq.gz' 'sample.fq.fastq.gz'"/> 717 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
700 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 718 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
701 <not_has_text text="modify" /> 719 <not_has_text text="modify" />
702 </assert_command> 720 </assert_command>
703 <assert_stderr>
704 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
705 </assert_stderr>
706 </test> 721 </test>
707 <!--Test 8: viral submission - User input metadata - Add extension = False--> 722 <!--Test 8: viral submission - User input metadata - Add extension = False-->
708 <test expect_failure="true"> 723 <test expect_failure="false">
709 <conditional name="action_options"> 724 <conditional name="action_options">
710 <param name="action" value="add"/> 725 <param name="action" value="add"/>
711 <section name="test_submit_parameters"> 726 <section name="test_submit_parameters">
712 <param name="submit_dev" value="false" /> 727 <param name="submit_dev" value="false" />
713 <param name="dry_run" value="false" /> 728 <param name="dry_run" value="true" />
714 </section> 729 </section>
715 <param name="test_submit" value="True"/> 730 <param name="test_submit" value="True"/>
716 <conditional name="input_format_conditional"> 731 <conditional name="input_format_conditional">
717 <param name="add_extension" value="False"/> 732 <param name="add_extension" value="false"/>
718 <param name="input_format" value="build_tables"/> 733 <param name="input_format" value="build_tables"/>
719 <conditional name="conditional_viral_metadata"> 734 <conditional name="conditional_viral_metadata">
720 <param name="viral_sample" value="true"/> 735 <param name="viral_sample" value="true"/>
721 <repeat name="rep_study"> 736 <repeat name="rep_study">
722 <param name="study_title" value="Test study title"/> 737 <param name="study_title" value="Test study title"/>
725 <param name="study_pubmed_id" value="Test study pubmedID"/> 740 <param name="study_pubmed_id" value="Test study pubmedID"/>
726 <repeat name="rep_sample"> 741 <repeat name="rep_sample">
727 <param name="sample_title" value="Test Sample title"/> 742 <param name="sample_title" value="Test Sample title"/>
728 <param name="sample_description" value="Test Sample description"/> 743 <param name="sample_description" value="Test Sample description"/>
729 <param name="scientific_name" value="Test Sample scientific name"/> 744 <param name="scientific_name" value="Test Sample scientific name"/>
730 <param name="tax_id" value="Test Sample tax_id"/> 745 <param name="tax_id" value="2697049"/>
731 <param name="collection_date" value="2020"/> 746 <param name="collection_date" value="2020"/>
732 <param name="geo_location_country" value="Belgium"/> 747 <param name="geo_location_country" value="Belgium"/>
733 <param name="host_common_name" value="Human"/> 748 <param name="host_common_name" value="Human"/>
734 <param name="host_subject_id" value="Patient_001"/> 749 <param name="host_subject_id" value="Patient_001"/>
735 <param name="host_health_state" value="healthy"/> 750 <param name="host_health_state" value="healthy"/>
764 <has_text_matching expression="ena-upload-cli"/> 779 <has_text_matching expression="ena-upload-cli"/>
765 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 780 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
766 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 781 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
767 <has_text_matching expression="--checklist ERC000033"/> 782 <has_text_matching expression="--checklist ERC000033"/>
768 </assert_command> 783 </assert_command>
769 <assert_stderr>
770 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
771 </assert_stderr>
772 </test> 784 </test>
773 <!--Test 9: modify option and auto compression - viral submission - User input metadata--> 785 <!--Test 9: modify option and auto compression - viral submission - User input metadata-->
774 <test expect_failure="true"> 786 <test expect_failure="false">
775 <conditional name="action_options"> 787 <conditional name="action_options">
776 <param name="action" value="modify"/> 788 <param name="action" value="modify"/>
777 <section name="test_submit_parameters"> 789 <section name="test_submit_parameters">
778 <param name="submit_dev" value="false" /> 790 <param name="submit_dev" value="false" />
779 <param name="dry_run" value="false" /> 791 <param name="dry_run" value="true" />
780 </section> 792 </section>
781 <param name="test_submit" value="True"/> 793 <param name="test_submit" value="True"/>
782 <conditional name="input_format_conditional"> 794 <conditional name="input_format_conditional">
783 <param name="add_extension" value="False"/> 795 <param name="add_extension" value="fasle"/>
784 <param name="input_format" value="build_tables"/> 796 <param name="input_format" value="build_tables"/>
785 <conditional name="conditional_viral_metadata"> 797 <conditional name="conditional_viral_metadata">
786 <param name="viral_sample" value="True"/> 798 <param name="viral_sample" value="True"/>
787 <repeat name="rep_study"> 799 <repeat name="rep_study">
788 <param name="study_title" value="Test study title"/> 800 <param name="study_title" value="Test study title"/>
791 <param name="study_pubmed_id" value="Test study pubmedID"/> 803 <param name="study_pubmed_id" value="Test study pubmedID"/>
792 <repeat name="rep_sample"> 804 <repeat name="rep_sample">
793 <param name="sample_title" value="Test Sample title"/> 805 <param name="sample_title" value="Test Sample title"/>
794 <param name="sample_description" value="Test Sample description"/> 806 <param name="sample_description" value="Test Sample description"/>
795 <param name="scientific_name" value="Test Sample scientific name"/> 807 <param name="scientific_name" value="Test Sample scientific name"/>
796 <param name="tax_id" value="Test Sample tax_id"/> 808 <param name="tax_id" value="2697049"/>
797 <param name="collection_date" value="2020"/> 809 <param name="collection_date" value="2020"/>
798 <param name="geo_location_country" value="Belgium"/> 810 <param name="geo_location_country" value="Belgium"/>
799 <param name="host_common_name" value="Human"/> 811 <param name="host_common_name" value="Human"/>
800 <param name="host_subject_id" value="Patient_001"/> 812 <param name="host_subject_id" value="Patient_001"/>
801 <param name="host_health_state" value="healthy"/> 813 <param name="host_health_state" value="healthy"/>
815 <param name="library_construction_protocol" value="Test library construction"/> 827 <param name="library_construction_protocol" value="Test library construction"/>
816 <param name="platform" value="ILLUMINA"/> 828 <param name="platform" value="ILLUMINA"/>
817 <param name="instrument_model" value="Illumina HiSeq 4000"/> 829 <param name="instrument_model" value="Illumina HiSeq 4000"/>
818 <repeat name="rep_runs"> 830 <repeat name="rep_runs">
819 <param name="run_base_name" value="run_from_hospital_X"/> 831 <param name="run_base_name" value="run_from_hospital_X"/>
820 <param name="upload_files" value="sample.fq" ftype="fastqsanger"/> 832 <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/>
821 </repeat> 833 </repeat>
822 </repeat> 834 </repeat>
823 </repeat> 835 </repeat>
824 </repeat> 836 </repeat>
825 </conditional> 837 </conditional>
826 </conditional> 838 </conditional>
827 </conditional> 839 </conditional>
828 <param name="center" value="Some research center"/> 840 <param name="center" value="Some research center"/>
829 <assert_command> 841 <assert_command>
830 <has_text_matching expression="ena-upload-cli"/> 842 <has_text_matching expression="ena-upload-cli"/>
831 <has_text_matching expression="--data 'sample.fq.gz'"/> 843 <has_text_matching expression="--data '1.fastqsanger.gz'"/>
832 <has_text_matching expression="--action 'modify' --center 'Some research center'"/> 844 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
833 <has_text_matching expression="--checklist ERC000033"/> 845 <has_text_matching expression="--checklist ERC000033"/>
834 <not_has_text text="add" /> 846 <not_has_text text="add" />
835 </assert_command> 847 </assert_command>
836 <assert_stderr>
837 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
838 </assert_stderr>
839 </test> 848 </test>
840 </tests> 849 </tests>
841 <help><![CDATA[ 850 <help><![CDATA[
842 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli 851 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
843 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 852 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
844 It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing 853 It is also possible to submit an excel file by following the template in https://github.com/ELIXIR-Belgium/ENA-metadata-templates
845 For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing
846 ]]></help> 854 ]]></help>
847 <citations> 855 <citations>
848 </citations> 856 </citations>
849 </tool> 857 </tool>