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comparison ena_upload.xml @ 11:f803a68fc9e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
author iuc
date Sat, 23 Mar 2024 22:06:45 +0000
parents 480d9e9d156b
children ea5e944f447d
comparison
equal deleted inserted replaced
10:480d9e9d156b 11:f803a68fc9e5
1 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" 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="@TOOL_VERSION@">0.6.3</token> 4 <token name="@TOOL_VERSION@">0.7.1</token>
4 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
5 <import>samples_macros.xml</import> 6 <import>samples_macros.xml</import>
6 </macros> 7 </macros>
7 <requirements> 8 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement>
46 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 &&
47 #end if 48 #end if
48 #if $action_options.input_format_conditional.input_format == "excel_tables": 49 #if $action_options.input_format_conditional.input_format == "excel_tables":
49 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx && 50 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
50 #end if 51 #end if
51 #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":
52 webin_id=`grep 'username' $credentials`; 56 webin_id=`grep 'username' $credentials`;
53 if [ "\$webin_id" = "" ]; then 57 if [ "\$webin_id" = "" ]; then
54 ## No credentials in user defined preferences 58 ## No credentials in user defined preferences
55 ## Fallback to global defined credentials (if exist) 59 ## Fallback to global defined credentials (if exist)
56 #import os 60 #import os
169 $files_to_upload.append(str($safename_reads_file)) 173 $files_to_upload.append(str($safename_reads_file))
170 #end for 174 #end for
171 #end if 175 #end if
172 #end if 176 #end if
173 177
174 #if $action_options.action == "add":
175 ena-upload-cli 178 ena-upload-cli
176 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy' 179 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy'
177 --action '$action_options.action' 180 --action '$action_options.action'
178 --center '$action_options.center' 181 --center '$action_options.test_submit_parameters.center'
179 --secret \${credentials_path} 182 --secret \${credentials_path}
180 --data 183 --data
181 #for $dataset in $files_to_upload: 184 #for $dataset in $files_to_upload:
182 '$dataset' 185 '$dataset'
183 #end for 186 #end for
184 #if $action_options.test_submit_parameters.dry_run == "True": 187 #if $action_options.test_submit_parameters.dry_run == "True":
185 --draft 188 --draft
186 #end if 189 #end if
187 #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 $action_options.input_format_conditional.input_format == "build_tables":
188 --experiment '$experiments_table_path' 193 --experiment '$experiments_table_path'
189 --study '$studies_table_path' 194 --study '$studies_table_path'
190 --run '$runs_table_path' 195 --run '$runs_table_path'
191 --sample '$samples_table_path' 196 --sample '$samples_table_path'
192 #else 197 #elif $action_options.input_format_conditional.input_format == "isa_json":
193 --xlsx ./xlsx_input.xlsx 198 --isa_json ./isa_json_input.json
194 #end if 199 --isa_assay_stream '$isa_assay_stream'
195 --action add 200 #end if
196 #if $action_options.input_format_conditional.input_format == "user_generated_tables": 201 #if $action_options.input_format_conditional.input_format == "build_tables":
197 --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
198 #else: 207 #else:
199 #if $action_options.input_format_conditional.input_format == "build_tables": 208 --checklist $action_options.input_format_conditional.checklist_id
200 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
201 --checklist ERC000033
202 #end if
203 #else:
204 --checklist $action_options.input_format_conditional.checklist_id
205 #end if
206 #end if
207 #if $action_options.idempotent == "True":
208 --auto_action
209 #end if 209 #end if
210 #if $action_options.test_submit_parameters.submit_dev == "True": 210 #if $action_options.test_submit_parameters.submit_dev == "True":
211 -d 211 -d
212 #end if 212 #end if
213 >> '$output'; 213 >> '$output';
214 #end if 214
215
216
217
218 #if $action_options.action == "modify":
219 ena-upload-cli
220 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy'
221 --action '$action_options.action'
222 --center '$action_options.center'
223 --secret \${credentials_path}
224 --data
225 #for $dataset in $files_to_upload:
226 '$dataset'
227 #end for
228 #if $action_options.test_submit_parameters.dry_run == "True":
229 --draft
230 #end if
231 #if $action_options.input_format_conditional.input_format != "excel_tables":
232 --experiment '$experiments_table_path'
233 --study '$studies_table_path'
234 --run '$runs_table_path'
235 --sample '$samples_table_path'
236 #else
237 --xlsx ./xlsx_input.xlsx
238 --auto_action
239 #end if
240 --action 'modify'
241 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
242 --checklist $action_options.input_format_conditional.checklist_id
243 #else:
244 #if $action_options.input_format_conditional.input_format == "build_tables":
245 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
246 --checklist ERC000033
247 #end if
248 #else:
249 --checklist $action_options.input_format_conditional.checklist_id
250 #end if
251 #end if
252 >> '$output';
253 #end if
254 215
255 #if $action_options.test_submit_parameters.dry_run == "False": 216 #if $action_options.test_submit_parameters.dry_run == "False":
256 echo -e 'center_name\t$action_options.center' >> '$output'; 217 echo -e 'center_name\t$action_options.test_submit_parameters.center' >> '$output';
257 echo -e 'action_option\t$action_options.action' >> '$output'; 218 echo -e 'action_option\t$action_options.action' >> '$output';
258 #end if 219 #end if
259 220
260 ## copy updated files 221 ## copy updated files
261 #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":
262 ## 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
263 ## this applies for both draft and real submissions 224 ## this applies for both draft and real submissions
264 cp './ENA_template_experiment_updated.tsv' $experiments_table_out; 225 cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
265 cp './ENA_template_sample_updated.tsv' $samples_table_out; 226 cp './ENA_template_sample_updated.tsv' $samples_table_out;
266 cp './ENA_template_study_updated.tsv' $studies_table_out; 227 cp './ENA_template_study_updated.tsv' $studies_table_out;
267 cp './ENA_template_run_updated.tsv' $runs_table_out; 228 cp './ENA_template_run_updated.tsv' $runs_table_out;
319 </configfile> 280 </configfile>
320 </configfiles> 281 </configfiles>
321 <inputs> 282 <inputs>
322 <conditional name="action_options"> 283 <conditional name="action_options">
323 <param name="action" type="select" label="Action to execute"> 284 <param name="action" type="select" label="Action to execute">
324 <option value="add" selected="True">Add new data</option> 285 <option value="add" selected="True">Add new (meta)data</option>
325 <option value="modify">Modify metadata</option> 286 <option value="modify">Modify metadata</option>
326 </param> 287 </param>
327 <when value="add"> 288 <when value="add">
328 <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" />
329 <expand macro="test_submit_section"/> 290 <expand macro="table_inputs_macro" />
291 <expand macro="test_submit_section"/>
292 </when>
293 <when value="modify">
330 <param name="test_submit" type="hidden" value="False" /> 294 <param name="test_submit" type="hidden" value="False" />
331 <expand macro="table_inputs_macro" /> 295 <expand macro="table_inputs_macro" />
332 </when> 296 <expand macro="test_submit_section"/>
333 <when value="modify">
334 <expand macro="test_submit_section"/>
335 <param name="test_submit" type="hidden" value="False" />
336 <expand macro="table_inputs_macro" />
337 </when> 297 </when>
338 </conditional> 298 </conditional>
339 </inputs> 299 </inputs>
340 <outputs> 300 <outputs>
341 <data name="output" format="txt" label="ENA submission receipt"/> 301 <data name="output" format="txt" label="ENA submission receipt"/>
342 <data name="studies_table_out" format="tabular" label="Studies table"> 302 <data name="studies_table_out" format="tabular" label="Studies table">
343 <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>
344 </data> 304 </data>
345 <data name="samples_table_out" format="tabular" label="Samples table"> 305 <data name="samples_table_out" format="tabular" label="Samples table">
346 <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>
347 </data> 307 </data>
348 <data name="experiments_table_out" format="tabular" label="Experiments table"> 308 <data name="experiments_table_out" format="tabular" label="Experiments table">
349 <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>
350 </data> 310 </data>
351 <data name="runs_table_out" format="tabular" label="Runs table"> 311 <data name="runs_table_out" format="tabular" label="Runs table">
352 <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>
353 </data> 313 </data>
354 </outputs> 314 </outputs>
355 <tests> 315 <tests>
356 <!--Test 1: excel input of VIRAL samples --> 316 <!--Test 1: excel input of VIRAL samples -->
357 <test expect_num_outputs="5"> 317 <test expect_num_outputs="5">
358 <conditional name="action_options"> 318 <conditional name="action_options">
359 <param name="action" value="add"/> 319 <param name="action" value="add"/>
360 <section name="test_submit_parameters"> 320 <section name="test_submit_parameters">
321 <param name="center" value="Some research center"/>
361 <param name="submit_dev" value="False" /> 322 <param name="submit_dev" value="False" />
362 <param name="dry_run" value="True" /> 323 <param name="dry_run" value="True" />
363 </section> 324 </section>
364 <conditional name="input_format_conditional"> 325 <conditional name="input_format_conditional">
365 <param name="input_format" value="excel_tables"/> 326 <param name="input_format" value="excel_tables"/>
370 <param name="run_input_format" value="multiple_selection_list"/> 331 <param name="run_input_format" value="multiple_selection_list"/>
371 <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"/>
372 </conditional> 333 </conditional>
373 </conditional> 334 </conditional>
374 </conditional> 335 </conditional>
375 <param name="center" value="Some research center"/>
376 <output name="experiments_table_out"> 336 <output name="experiments_table_out">
377 <assert_contents> 337 <assert_contents>
378 <has_n_lines n="5"/> 338 <has_n_lines n="5"/>
379 <has_n_columns n="17"/> 339 <has_n_columns n="17"/>
380 <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"/>
406 <!--Test 2: excel input of VIRAL samples with extended columns--> 366 <!--Test 2: excel input of VIRAL samples with extended columns-->
407 <test expect_num_outputs="5"> 367 <test expect_num_outputs="5">
408 <conditional name="action_options"> 368 <conditional name="action_options">
409 <param name="action" value="add"/> 369 <param name="action" value="add"/>
410 <section name="test_submit_parameters"> 370 <section name="test_submit_parameters">
371 <param name="center" value="Some research center"/>
411 <param name="submit_dev" value="False" /> 372 <param name="submit_dev" value="False" />
412 <param name="dry_run" value="True" /> 373 <param name="dry_run" value="True" />
413 </section> 374 </section>
414 <conditional name="input_format_conditional"> 375 <conditional name="input_format_conditional">
415 <param name="input_format" value="excel_tables"/> 376 <param name="input_format" value="excel_tables"/>
420 <param name="run_input_format" value="multiple_selection_list"/> 381 <param name="run_input_format" value="multiple_selection_list"/>
421 <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"/>
422 </conditional> 383 </conditional>
423 </conditional> 384 </conditional>
424 </conditional> 385 </conditional>
425 <param name="center" value="Some research center"/>
426 <output name="experiments_table_out"> 386 <output name="experiments_table_out">
427 <assert_contents> 387 <assert_contents>
428 <has_n_lines n="5"/> 388 <has_n_lines n="5"/>
429 <has_n_columns n="17"/> 389 <has_n_columns n="17"/>
430 <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"/>
466 <!--Test 3: excel input of NON-VIRAL samples--> 426 <!--Test 3: excel input of NON-VIRAL samples-->
467 <test expect_num_outputs="5"> 427 <test expect_num_outputs="5">
468 <conditional name="action_options"> 428 <conditional name="action_options">
469 <param name="action" value="add"/> 429 <param name="action" value="add"/>
470 <section name="test_submit_parameters"> 430 <section name="test_submit_parameters">
431 <param name="center" value="Some research center"/>
471 <param name="submit_dev" value="False" /> 432 <param name="submit_dev" value="False" />
472 <param name="dry_run" value="True" /> 433 <param name="dry_run" value="True" />
473 </section> 434 </section>
474 <conditional name="input_format_conditional"> 435 <conditional name="input_format_conditional">
475 <param name="input_format" value="excel_tables"/> 436 <param name="input_format" value="excel_tables"/>
480 <param name="run_input_format" value="multiple_selection_list"/> 441 <param name="run_input_format" value="multiple_selection_list"/>
481 <param name="data" value="sample_no_extension"/> 442 <param name="data" value="sample_no_extension"/>
482 </conditional> 443 </conditional>
483 </conditional> 444 </conditional>
484 </conditional> 445 </conditional>
485 <param name="center" value="Some research center"/>
486 <output name="experiments_table_out"> 446 <output name="experiments_table_out">
487 <assert_contents> 447 <assert_contents>
488 <has_n_lines n="2"/> 448 <has_n_lines n="2"/>
489 <has_n_columns n="17"/> 449 <has_n_columns n="17"/>
490 <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"/>
516 <!--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 -->
517 <test expect_failure="True"> 477 <test expect_failure="True">
518 <conditional name="action_options"> 478 <conditional name="action_options">
519 <param name="action" value="add"/> 479 <param name="action" value="add"/>
520 <section name="test_submit_parameters"> 480 <section name="test_submit_parameters">
481 <param name="center" value="Some research center"/>
521 <param name="submit_dev" value="False" /> 482 <param name="submit_dev" value="False" />
522 <param name="dry_run" value="False" /> 483 <param name="dry_run" value="False" />
523 </section> 484 </section>
524 <conditional name="input_format_conditional"> 485 <conditional name="input_format_conditional">
525 <param name="add_extension" value="True"/> 486 <param name="add_extension" value="True"/>
539 </collection> 500 </collection>
540 </param> 501 </param>
541 </conditional> 502 </conditional>
542 </conditional> 503 </conditional>
543 </conditional> 504 </conditional>
544 <param name="center" value="Some research center"/>
545 <assert_command> 505 <assert_command>
546 <has_text_matching expression="ena-upload-cli"/> 506 <has_text_matching expression="ena-upload-cli"/>
547 <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'"/>
548 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 508 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
549 </assert_command> 509 </assert_command>
550 </test> 510 </test>
551 <!--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 -->
552 <test expect_failure="True"> 512 <test expect_failure="True">
553 <conditional name="action_options"> 513 <conditional name="action_options">
554 <param name="action" value="add"/> 514 <param name="action" value="add"/>
555 <section name="test_submit_parameters"> 515 <section name="test_submit_parameters">
516 <param name="center" value="Some research center"/>
556 <param name="submit_dev" value="False" /> 517 <param name="submit_dev" value="False" />
557 <param name="dry_run" value="False" /> 518 <param name="dry_run" value="False" />
558 </section> 519 </section>
559 <param name="idempotent" value="True"/>
560 <conditional name="input_format_conditional"> 520 <conditional name="input_format_conditional">
561 <param name="add_extension" value="True"/> 521 <param name="add_extension" value="True"/>
562 <param name="input_format" value="excel_tables"/> 522 <param name="input_format" value="excel_tables"/>
563 <param name="checklist_id" value="ERC000011"/> 523 <param name="checklist_id" value="ERC000011"/>
564 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> 524 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
575 </collection> 535 </collection>
576 </param> 536 </param>
577 </conditional> 537 </conditional>
578 </conditional> 538 </conditional>
579 </conditional> 539 </conditional>
580 <param name="center" value="Some research center"/>
581 <assert_command> 540 <assert_command>
582 <has_text_matching expression="ena-upload-cli"/> 541 <has_text_matching expression="ena-upload-cli"/>
583 <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'"/>
584 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 543 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
585 <has_text_matching expression="--auto_action"/>
586 </assert_command> 544 </assert_command>
587 </test> 545 </test>
588 <!--Test 5: build tables from user input fields NON-VIRAL samples--> 546 <!--Test 5: build tables from user input fields NON-VIRAL samples-->
589 <test expect_num_outputs="5"> 547 <test expect_num_outputs="5">
590 <conditional name="action_options"> 548 <conditional name="action_options">
591 <param name="action" value="add"/> 549 <param name="action" value="add"/>
592 <section name="test_submit_parameters"> 550 <section name="test_submit_parameters">
551 <param name="center" value="Some research center"/>
593 <param name="submit_dev" value="False" /> 552 <param name="submit_dev" value="False" />
594 <param name="dry_run" value="True" /> 553 <param name="dry_run" value="True" />
595 </section> 554 </section>
596 <conditional name="input_format_conditional"> 555 <conditional name="input_format_conditional">
597 <param name="input_format" value="build_tables"/> 556 <param name="input_format" value="build_tables"/>
628 </repeat> 587 </repeat>
629 </repeat> 588 </repeat>
630 </conditional> 589 </conditional>
631 </conditional> 590 </conditional>
632 </conditional> 591 </conditional>
633 <param name="center" value="Some research center"/>
634 <output name="experiments_table_out"> 592 <output name="experiments_table_out">
635 <assert_contents> 593 <assert_contents>
636 <has_n_lines n="2"/> 594 <has_n_lines n="2"/>
637 <has_n_columns n="17"/> 595 <has_n_columns n="17"/>
638 </assert_contents> 596 </assert_contents>
662 also tests compression of uncompressed inputs and adding the .gz suffix --> 620 also tests compression of uncompressed inputs and adding the .gz suffix -->
663 <test expect_failure="False" expect_num_outputs="5"> 621 <test expect_failure="False" expect_num_outputs="5">
664 <conditional name="action_options"> 622 <conditional name="action_options">
665 <param name="action" value="add"/> 623 <param name="action" value="add"/>
666 <section name="test_submit_parameters"> 624 <section name="test_submit_parameters">
625 <param name="center" value="Some research center"/>
667 <param name="submit_dev" value="True" /> 626 <param name="submit_dev" value="True" />
668 <param name="dry_run" value="True" /> 627 <param name="dry_run" value="True" />
669 </section> 628 </section>
670 <param name="test_submit" value="True"/> 629 <param name="test_submit" value="True"/>
671 <conditional name="input_format_conditional"> 630 <conditional name="input_format_conditional">
704 </repeat> 663 </repeat>
705 </repeat> 664 </repeat>
706 </conditional> 665 </conditional>
707 </conditional> 666 </conditional>
708 </conditional> 667 </conditional>
709 <param name="center" value="Some research center"/>
710 <assert_command> 668 <assert_command>
711 <has_text_matching expression="ena-upload-cli"/> 669 <has_text_matching expression="ena-upload-cli"/>
712 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 670 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
713 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 671 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
714 <not_has_text text="modify" /> 672 <not_has_text text="modify" />
717 <!--Test 7: viral submission - User input metadata - Add extension = False--> 675 <!--Test 7: viral submission - User input metadata - Add extension = False-->
718 <test expect_failure="False" expect_num_outputs="5"> 676 <test expect_failure="False" expect_num_outputs="5">
719 <conditional name="action_options"> 677 <conditional name="action_options">
720 <param name="action" value="add"/> 678 <param name="action" value="add"/>
721 <section name="test_submit_parameters"> 679 <section name="test_submit_parameters">
680 <param name="center" value="Some research center"/>
722 <param name="submit_dev" value="False" /> 681 <param name="submit_dev" value="False" />
723 <param name="dry_run" value="True" /> 682 <param name="dry_run" value="True" />
724 </section> 683 </section>
725 <param name="test_submit" value="True"/> 684 <param name="test_submit" value="True"/>
726 <conditional name="input_format_conditional"> 685 <conditional name="input_format_conditional">
767 </repeat> 726 </repeat>
768 </repeat> 727 </repeat>
769 </conditional> 728 </conditional>
770 </conditional> 729 </conditional>
771 </conditional> 730 </conditional>
772 <param name="center" value="Some research center"/>
773 <assert_command> 731 <assert_command>
774 <has_text_matching expression="ena-upload-cli"/> 732 <has_text_matching expression="ena-upload-cli"/>
775 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 733 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
776 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 734 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
777 <has_text_matching expression="--checklist ERC000033"/> 735 <has_text_matching expression="--checklist ERC000033"/>
780 <!--Test 8: modify option and auto compression - viral submission - User input metadata--> 738 <!--Test 8: modify option and auto compression - viral submission - User input metadata-->
781 <test expect_failure="False" expect_num_outputs="5"> 739 <test expect_failure="False" expect_num_outputs="5">
782 <conditional name="action_options"> 740 <conditional name="action_options">
783 <param name="action" value="modify"/> 741 <param name="action" value="modify"/>
784 <section name="test_submit_parameters"> 742 <section name="test_submit_parameters">
743 <param name="center" value="Some research center"/>
785 <param name="submit_dev" value="False" /> 744 <param name="submit_dev" value="False" />
786 <param name="dry_run" value="True" /> 745 <param name="dry_run" value="True" />
787 </section> 746 </section>
788 <param name="test_submit" value="True"/> 747 <param name="test_submit" value="True"/>
789 <conditional name="input_format_conditional"> 748 <conditional name="input_format_conditional">
830 </repeat> 789 </repeat>
831 </repeat> 790 </repeat>
832 </conditional> 791 </conditional>
833 </conditional> 792 </conditional>
834 </conditional> 793 </conditional>
835 <param name="center" value="Some research center"/>
836 <assert_command> 794 <assert_command>
837 <has_text_matching expression="ena-upload-cli"/> 795 <has_text_matching expression="ena-upload-cli"/>
838 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 796 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
839 <has_text_matching expression="--action 'modify' --center 'Some research center'"/> 797 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
840 <has_text_matching expression="--checklist ERC000033"/> 798 <has_text_matching expression="--checklist ERC000033"/>
841 <not_has_text text="add" /> 799 <not_has_text text="add" />
842 </assert_command> 800 </assert_command>
843 </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\tsubmission_date\tfile_checksum"/>
847 </assert_contents>
848 </output>
849 </test>
844 </tests> 850 </tests>
845 <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.
846 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli 852
847 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. 853 .. class:: warningmark
848 ]]></help> 854
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>
849 <citations> 856 <citations>
850 <citation type="doi">doi:10.1093/bioinformatics/btab421</citation> 857 <citation type="doi">doi:10.1093/bioinformatics/btab421</citation>
851 </citations> 858 </citations>
852 </tool> 859 </tool>