Mercurial > repos > ieguinoa > ena_upload
comparison ena_upload.xml @ 0:5d59238cd3f4 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Wed, 02 Feb 2022 17:16:15 +0000 |
| parents | |
| children | 2f7a70c0d3ab |
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| -1:000000000000 | 0:5d59238cd3f4 |
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| 1 <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT"> | |
| 2 <macros> | |
| 3 <token name="@VERSION@">0.5.3</token> | |
| 4 <import>samples_macros.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement> | |
| 8 </requirements> | |
| 9 <stdio> | |
| 10 <regex match="Oops" source="stderr" level="fatal"/> | |
| 11 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/> | |
| 12 </stdio> | |
| 13 <command detect_errors="exit_code"><![CDATA[ | |
| 14 mkdir ./submission_files; | |
| 15 #set $studies_table_path = './submission_files/studies.tsv' | |
| 16 #set $samples_table_path = './submission_files/samples.tsv' | |
| 17 #set $experiments_table_path = './submission_files/experiments.tsv' | |
| 18 #set $runs_table_path = './submission_files/runs.tsv' | |
| 19 | |
| 20 #set $studies_table_path_updated = './submission_files/studies_updated.tsv' | |
| 21 #set $samples_table_path_updated = './submission_files/samples_updated.tsv' | |
| 22 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv' | |
| 23 #set $runs_table_path_updated = './submission_files/runs_updated.tsv' | |
| 24 | |
| 25 #set working_dir = os.getcwd() | |
| 26 #if $action_options.input_format_conditional.input_format == "build_tables": | |
| 27 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json; | |
| 28 #end if | |
| 29 | |
| 30 | |
| 31 #if $action_options.input_format_conditional.input_format == "build_tables": | |
| 32 cp $studies_table_path $studies_table_out && | |
| 33 cp $samples_table_path $samples_table_out && | |
| 34 cp $experiments_table_path $experiments_table_out && | |
| 35 cp $runs_table_path $runs_table_out && | |
| 36 #end if | |
| 37 #if $action_options.input_format_conditional.input_format == "user_generated_tables": | |
| 38 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path && | |
| 39 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path && | |
| 40 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path && | |
| 41 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path && | |
| 42 #end if | |
| 43 #if $action_options.input_format_conditional.input_format == "excel_tables": | |
| 44 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx && | |
| 45 #end if | |
| 46 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False": | |
| 47 webin_id=`grep 'username' $credentials`; | |
| 48 if [ "\$webin_id" = "" ]; then | |
| 49 ## No credentials in user defined preferences | |
| 50 ## Fallback to global defined credentials (if exist) | |
| 51 #import os | |
| 52 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): | |
| 53 credentials_path=\${GALAXY_ENA_SECRETS}; | |
| 54 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`; | |
| 55 if [ "\$webin_id" = "" ]; then | |
| 56 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information"; | |
| 57 exit 1; | |
| 58 fi; | |
| 59 #else: | |
| 60 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information"; | |
| 61 exit 1; | |
| 62 #end if | |
| 63 else | |
| 64 credentials_path='$credentials'; | |
| 65 fi; | |
| 66 #end if | |
| 67 | |
| 68 #if $action_options.test_submit == "True" or $action_options.test_submit_parameters.dry_run == "true": | |
| 69 credentials_path='test_fake_path'; | |
| 70 #if $action_options.test_submit_parameters.dry_run == "true" and $action_options.input_format_conditional.input_format == "excel_tables": | |
| 71 echo "username: test_user" > \$credentials_path; | |
| 72 echo "password: test_password" >> \$credentials_path; | |
| 73 #end if | |
| 74 #end if | |
| 75 | |
| 76 ## create the list of files to upload and make the symlinks | |
| 77 #import re | |
| 78 #set $files_to_upload = list() | |
| 79 #if $action_options.input_format_conditional.input_format == "build_tables": | |
| 80 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study: | |
| 81 #for $sample in $study.rep_sample: | |
| 82 #for $experiment in $sample.rep_experiment: | |
| 83 #for $run in $experiment.rep_runs: | |
| 84 #for $file in $run.upload_files: | |
| 85 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) | |
| 86 #if $action_options.input_format_conditional.add_extension == "true": | |
| 87 #set $extension = '.fastq' | |
| 88 #else | |
| 89 #set $extension = '' | |
| 90 #end if | |
| 91 #if $file.is_of_type('fastq', 'fastqsanger'): | |
| 92 ## compression output is defined as safename_reads_file so no need to symlink | |
| 93 #set $safename_reads_file = $safename_reads_file + $extension + '.gz' | |
| 94 gzip -c '$file' > $safename_reads_file && | |
| 95 #else: | |
| 96 #if $action_options.input_format_conditional.add_extension == "true": | |
| 97 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): | |
| 98 #set $compression = '.gz' | |
| 99 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): | |
| 100 #set $compression = '.bz2' | |
| 101 #end if | |
| 102 #set $safename_reads_file = $safename_reads_file + $extension + $compression | |
| 103 #end if | |
| 104 ln -s '$file' $safename_reads_file && | |
| 105 #end if | |
| 106 $files_to_upload.append(str($safename_reads_file)) | |
| 107 #end for | |
| 108 #end for | |
| 109 #end for | |
| 110 #end for | |
| 111 #end for | |
| 112 #else: | |
| 113 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list': | |
| 114 #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection: | |
| 115 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name) | |
| 116 ## Always need to add .fastq + compression suffix because the name is based on the pair name which has no extensions | |
| 117 #if $pair.forward.is_of_type('fastq', 'fastqsanger'): | |
| 118 ## compress the file, no need to create the link then | |
| 119 ## always add the compression suffix (.gz) | |
| 120 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz' | |
| 121 gzip -c '$file' > $safename_fwd_reads_file && | |
| 122 #else | |
| 123 #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'): | |
| 124 #set $compression = '.gz' | |
| 125 #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'): | |
| 126 #set $compression = '.bz2' | |
| 127 #end if | |
| 128 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression | |
| 129 ln -s '$pair.forward' $safename_fwd_reads_file && | |
| 130 #end if | |
| 131 | |
| 132 #if $pair.reverse.is_of_type('fastq', 'fastqsanger'): | |
| 133 ## compress the file, no need to create the link then | |
| 134 #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz' | |
| 135 gzip -c '$file' > $safename_rev_reads_file && | |
| 136 #else | |
| 137 #if $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'): | |
| 138 #set $compression = '.bz2' | |
| 139 #elif $pair.reverse.is_of_type('fastqsanger.gz', 'fastq.gz'): | |
| 140 #set $compression = '.gz' | |
| 141 #end if | |
| 142 #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression | |
| 143 ln -s '$pair.reverse' $safename_rev_reads_file && | |
| 144 #end if | |
| 145 $files_to_upload.append(str($safename_fwd_reads_file)) | |
| 146 $files_to_upload.append(str($safename_rev_reads_file)) | |
| 147 #end for | |
| 148 #end if | |
| 149 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list': | |
| 150 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data: | |
| 151 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) | |
| 152 #if $file.is_of_type('fastq', 'fastqsanger'): | |
| 153 ## always compress add the gz extension | |
| 154 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true": | |
| 155 #set $safename_reads_file = $safename_reads_file + '.fastq.gz' | |
| 156 #else | |
| 157 #set $safename_reads_file = $safename_reads_file + '.gz' | |
| 158 #end if | |
| 159 gzip -c '$file' > $safename_reads_file && | |
| 160 #else | |
| 161 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true": | |
| 162 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): | |
| 163 #set $extension = '.fastq.gz' | |
| 164 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): | |
| 165 #set $extension = '.fastq.bz2' | |
| 166 #end if | |
| 167 #set $safename_reads_file = $safename_reads_file + $extension | |
| 168 #end if | |
| 169 ln -s '$file' $safename_reads_file && | |
| 170 #end if | |
| 171 $files_to_upload.append(str($safename_reads_file)) | |
| 172 #end for | |
| 173 #end if | |
| 174 #end if | |
| 175 | |
| 176 | |
| 177 #if $action_options.test_submit_parameters.dry_run == "false" or $action_options.input_format_conditional.input_format == "excel_tables": | |
| 178 #if $action_options.action == "add": | |
| 179 ena-upload-cli | |
| 180 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' | |
| 181 --action '$action_options.action' | |
| 182 --center '$action_options.center' | |
| 183 --secret \${credentials_path} | |
| 184 --data | |
| 185 #for $dataset in $files_to_upload: | |
| 186 '$dataset' | |
| 187 #end for | |
| 188 #if $action_options.test_submit_parameters.dry_run == "true": | |
| 189 --draft | |
| 190 #end if | |
| 191 #if $action_options.input_format_conditional.input_format != "excel_tables": | |
| 192 --experiment '$experiments_table_path' | |
| 193 --study '$studies_table_path' | |
| 194 --run '$runs_table_path' | |
| 195 --sample '$samples_table_path' | |
| 196 #else | |
| 197 --xlsx ./xlsx_input.xlsx | |
| 198 #end if | |
| 199 --action add | |
| 200 #if $action_options.input_format_conditional.input_format == "user_generated_tables": | |
| 201 --checklist $action_options.input_format_conditional.checklist_id | |
| 202 #else: | |
| 203 #if $action_options.input_format_conditional.input_format == "build_tables": | |
| 204 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": | |
| 205 --checklist ERC000033 | |
| 206 #end if | |
| 207 #else: | |
| 208 --checklist $action_options.input_format_conditional.checklist_id | |
| 209 #end if | |
| 210 #end if | |
| 211 | |
| 212 #if $action_options.test_submit_parameters.submit_dev == "true": | |
| 213 -d | |
| 214 #end if | |
| 215 >> '$output'; | |
| 216 #end if | |
| 217 | |
| 218 #if $action_options.action == "modify": | |
| 219 ena-upload-cli | |
| 220 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' | |
| 221 --action '$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 #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'; | |
| 257 #if $action_options.input_format_conditional.input_format == "build_tables": | |
| 258 cp $studies_table_path_updated $studies_table_out 2>/dev/null; | |
| 259 cp $samples_table_path_updated $samples_table_out 2>/dev/null; | |
| 260 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null; | |
| 261 cp $runs_table_path_updated $runs_table_out 2>/dev/null; | |
| 262 #end if | |
| 263 #else | |
| 264 ## for the excel input case, copy the upload-cli generated tables to the output files | |
| 265 ## this applies for both draft and real submissions | |
| 266 cp './ENA_template_experiment_updated.tsv' $experiments_table_out; | |
| 267 cp './ENA_template_sample_updated.tsv' $samples_table_out; | |
| 268 cp './ENA_template_study_updated.tsv' $studies_table_out; | |
| 269 cp './ENA_template_run_updated.tsv' $runs_table_out; | |
| 270 #end if | |
| 271 #else: | |
| 272 exit 0; | |
| 273 #end if | |
| 274 | |
| 275 ]]></command> | |
| 276 <configfiles> | |
| 277 <configfile name="credentials"><![CDATA[ | |
| 278 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip() | |
| 279 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip() | |
| 280 #if $webin_id != "": | |
| 281 username: "$webin_id" | |
| 282 password: "$password" | |
| 283 #end if | |
| 284 ]]></configfile> | |
| 285 <configfile name="studies_json"> | |
| 286 #import json | |
| 287 #import re | |
| 288 #if $action_options.input_format_conditional.input_format == "build_tables": | |
| 289 #set $files_to_upload = list() | |
| 290 #set $studies = list() | |
| 291 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study: | |
| 292 #set samples = list() | |
| 293 #for $sample in $study.rep_sample: | |
| 294 #set experiments = list() | |
| 295 #for $experiment in $sample.rep_experiment: | |
| 296 #set runs = list() | |
| 297 #for $run in $experiment.rep_runs: | |
| 298 #set run_files = list() | |
| 299 #for $file in $run.upload_files: | |
| 300 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) | |
| 301 $run_files.append(str($safename_reads_file)) | |
| 302 #end for | |
| 303 $runs.append((str($run.run_base_name),$run_files)) | |
| 304 #end for | |
| 305 | |
| 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}) | |
| 307 #end for | |
| 308 #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}) | |
| 311 #else: | |
| 312 | |
| 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 | |
| 315 #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}) | |
| 317 #end for | |
| 318 #echo $json.dumps($studies) | |
| 319 #end if | |
| 320 </configfile> | |
| 321 </configfiles> | |
| 322 <inputs> | |
| 323 <conditional name="action_options"> | |
| 324 <param name="action" type="select" label="Action to execute"> | |
| 325 <option value="add" selected="True">Add new data</option> | |
| 326 <option value="modify">Modify metadata</option> | |
| 327 </param> | |
| 328 <when value="add"> | |
| 329 <expand macro="test_submit_section"/> | |
| 330 <param name="test_submit" type="hidden" value="False" /> | |
| 331 <expand macro="table_inputs_macro" /> | |
| 332 </when> | |
| 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> | |
| 338 </conditional> | |
| 339 </inputs> | |
| 340 <outputs> | |
| 341 <data name="output" format="txt" label="ENA submission receipt"/> | |
| 342 <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> | |
| 344 </data> | |
| 345 <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> | |
| 347 </data> | |
| 348 <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> | |
| 350 </data> | |
| 351 <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> | |
| 353 </data> | |
| 354 </outputs> | |
| 355 <tests> | |
| 356 <!--Test 1: excel input of VIRAL samples --> | |
| 357 <test> | |
| 358 <conditional name="action_options"> | |
| 359 <param name="action" value="add"/> | |
| 360 <section name="test_submit_parameters"> | |
| 361 <param name="submit_dev" value="false" /> | |
| 362 <param name="dry_run" value="true" /> | |
| 363 </section> | |
| 364 <conditional name="input_format_conditional"> | |
| 365 <param name="input_format" value="excel_tables"/> | |
| 366 <param name="checklist_id" value="ERC000033"/> | |
| 367 <param name="xlsx_file" value="metadata_test_viral.xlsx"/> | |
| 368 <conditional name="run_input_format_conditional"> | |
| 369 <param name="add_extension" value="false"/> | |
| 370 <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"/> | |
| 372 </conditional> | |
| 373 </conditional> | |
| 374 </conditional> | |
| 375 <param name="center" value="Some research center"/> | |
| 376 <output name="experiments_table_out"> | |
| 377 <assert_contents> | |
| 378 <has_n_lines n="5"/> | |
| 379 <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"/> | |
| 381 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> | |
| 382 </assert_contents> | |
| 383 </output> | |
| 384 <output name="studies_table_out"> | |
| 385 <assert_contents> | |
| 386 <has_n_lines n="2"/> | |
| 387 <has_n_columns n="7"/> | |
| 388 <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(.*)"/> | |
| 389 </assert_contents> | |
| 390 </output> | |
| 391 <output name="samples_table_out"> | |
| 392 <assert_contents> | |
| 393 <has_n_lines n="5"/> | |
| 394 <has_n_columns n="18"/> | |
| 395 </assert_contents> | |
| 396 </output> | |
| 397 <output name="runs_table_out"> | |
| 398 <assert_contents> | |
| 399 <has_n_lines n="5"/> | |
| 400 <has_n_columns n="8"/> | |
| 401 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> | |
| 402 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> | |
| 403 </assert_contents> | |
| 404 </output> | |
| 405 </test> | |
| 406 <!--Test 2: excel input of VIRAL samples with extended columns--> | |
| 407 <test> | |
| 408 <conditional name="action_options"> | |
| 409 <param name="action" value="add"/> | |
| 410 <section name="test_submit_parameters"> | |
| 411 <param name="submit_dev" value="false" /> | |
| 412 <param name="dry_run" value="true" /> | |
| 413 </section> | |
| 414 <conditional name="input_format_conditional"> | |
| 415 <param name="input_format" value="excel_tables"/> | |
| 416 <param name="checklist_id" value="ERC000033"/> | |
| 417 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/> | |
| 418 <conditional name="run_input_format_conditional"> | |
| 419 <param name="add_extension" value="false"/> | |
| 420 <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"/> | |
| 422 </conditional> | |
| 423 </conditional> | |
| 424 </conditional> | |
| 425 <param name="center" value="Some research center"/> | |
| 426 <output name="experiments_table_out"> | |
| 427 <assert_contents> | |
| 428 <has_n_lines n="5"/> | |
| 429 <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"/> | |
| 431 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> | |
| 432 </assert_contents> | |
| 433 </output> | |
| 434 <output name="studies_table_out"> | |
| 435 <assert_contents> | |
| 436 <has_n_lines n="2"/> | |
| 437 <has_n_columns n="7"/> | |
| 438 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/> | |
| 439 <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(.*)"/> | |
| 440 </assert_contents> | |
| 441 </output> | |
| 442 <output name="samples_table_out"> | |
| 443 <assert_contents> | |
| 444 <has_n_lines n="5"/> | |
| 445 <has_n_columns n="43"/> | |
| 446 </assert_contents> | |
| 447 </output> | |
| 448 <output name="runs_table_out"> | |
| 449 <assert_contents> | |
| 450 <has_n_lines n="5"/> | |
| 451 <has_n_columns n="8"/> | |
| 452 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> | |
| 453 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> | |
| 454 </assert_contents> | |
| 455 </output> | |
| 456 </test> | |
| 457 <!--Test 3: excel input of NON-VIRAL samples--> | |
| 458 <test> | |
| 459 <conditional name="action_options"> | |
| 460 <param name="action" value="add"/> | |
| 461 <section name="test_submit_parameters"> | |
| 462 <param name="submit_dev" value="false" /> | |
| 463 <param name="dry_run" value="true" /> | |
| 464 </section> | |
| 465 <conditional name="input_format_conditional"> | |
| 466 <param name="input_format" value="excel_tables"/> | |
| 467 <param name="checklist_id" value="ERC000011"/> | |
| 468 <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/> | |
| 469 <conditional name="run_input_format_conditional"> | |
| 470 <param name="add_extension" value="true"/> | |
| 471 <param name="run_input_format" value="multiple_selection_list"/> | |
| 472 <param name="data" value="sample_no_extension"/> | |
| 473 </conditional> | |
| 474 </conditional> | |
| 475 </conditional> | |
| 476 <param name="center" value="Some research center"/> | |
| 477 <output name="experiments_table_out"> | |
| 478 <assert_contents> | |
| 479 <has_n_lines n="2"/> | |
| 480 <has_n_columns n="17"/> | |
| 481 <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"/> | |
| 482 </assert_contents> | |
| 483 </output> | |
| 484 <output name="studies_table_out"> | |
| 485 <assert_contents> | |
| 486 <has_n_lines n="2"/> | |
| 487 <has_n_columns n="7"/> | |
| 488 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/> | |
| 489 </assert_contents> | |
| 490 </output> | |
| 491 <output name="samples_table_out"> | |
| 492 <assert_contents> | |
| 493 <has_n_lines n="2"/> | |
| 494 <has_n_columns n="8"/> | |
| 495 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/> | |
| 496 </assert_contents> | |
| 497 </output> | |
| 498 <output name="runs_table_out"> | |
| 499 <assert_contents> | |
| 500 <has_n_lines n="2"/> | |
| 501 <has_n_columns n="8"/> | |
| 502 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> | |
| 503 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/> | |
| 504 </assert_contents> | |
| 505 </output> | |
| 506 </test> | |
| 507 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection --> | |
| 508 <test expect_failure="true"> | |
| 509 <conditional name="action_options"> | |
| 510 <param name="action" value="add"/> | |
| 511 <section name="test_submit_parameters"> | |
| 512 <param name="submit_dev" value="false" /> | |
| 513 <param name="dry_run" value="false" /> | |
| 514 </section> | |
| 515 <conditional name="input_format_conditional"> | |
| 516 <param name="add_extension" value="true"/> | |
| 517 <param name="input_format" value="excel_tables"/> | |
| 518 <param name="checklist_id" value="ERC000011"/> | |
| 519 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> | |
| 520 <conditional name="run_input_format_conditional"> | |
| 521 <param name="run_input_format" value="paired_list"/> | |
| 522 <param name="paired_end_collection"> | |
| 523 <collection type="list:paired"> | |
| 524 <element name="paired_run_name"> | |
| 525 <collection type="paired"> | |
| 526 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" /> | |
| 527 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" /> | |
| 528 </collection> | |
| 529 </element> | |
| 530 </collection> | |
| 531 </param> | |
| 532 </conditional> | |
| 533 </conditional> | |
| 534 </conditional> | |
| 535 <param name="center" value="Some research center"/> | |
| 536 <assert_command> | |
| 537 <has_text_matching expression="ena-upload-cli"/> | |
| 538 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/> | |
| 539 <has_text_matching expression="--action 'add' --center 'Some research center'"/> | |
| 540 </assert_command> | |
| 541 </test> | |
| 542 <!--Test 5: build tables from user input fields NON-VIRAL samples--> | |
| 543 <test> | |
| 544 <conditional name="action_options"> | |
| 545 <param name="action" value="add"/> | |
| 546 <section name="test_submit_parameters"> | |
| 547 <param name="submit_dev" value="false" /> | |
| 548 <param name="dry_run" value="true" /> | |
| 549 </section> | |
| 550 <conditional name="input_format_conditional"> | |
| 551 <param name="input_format" value="build_tables"/> | |
| 552 <param name="add_extension" value="true"/> | |
| 553 <conditional name="conditional_viral_metadata"> | |
| 554 <param name="viral_sample" value="False"/> | |
| 555 <repeat name="rep_study"> | |
| 556 <param name="study_title" value="Test study title"/> | |
| 557 <param name="study_abstract" value="Test study abstract"/> | |
| 558 <param name="study_type" value="Epigenetics"/> | |
| 559 <param name="study_pubmed_id" value="Test study pubmedID"/> | |
| 560 <repeat name="rep_sample"> | |
| 561 <param name="sample_title" value="Test Sample title"/> | |
| 562 <param name="sample_description" value="Test Sample description"/> | |
| 563 <param name="scientific_name" value="Test Sample scientific name"/> | |
| 564 <param name="tax_id" value="Test Sample tax_id"/> | |
| 565 <repeat name="rep_experiment"> | |
| 566 <param name="experiment_title" value="Test experiment title"/> | |
| 567 <param name="experiment_design" value="Test experiment design description"/> | |
| 568 <param name="library_strategy" value="CTS"/> | |
| 569 <param name="library_source" value="GENOMIC"/> | |
| 570 <param name="library_selection" value="PCR"/> | |
| 571 <param name="library_layout" value="SINGLE"/> | |
| 572 <param name="insert_size" value="150"/> | |
| 573 <param name="library_construction_protocol" value="Test library construction"/> | |
| 574 <param name="platform" value="ILLUMINA"/> | |
| 575 <param name="instrument_model" value="Illumina HiSeq 4000"/> | |
| 576 <repeat name="rep_runs"> | |
| 577 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> | |
| 578 </repeat> | |
| 579 </repeat> | |
| 580 </repeat> | |
| 581 </repeat> | |
| 582 </conditional> | |
| 583 </conditional> | |
| 584 </conditional> | |
| 585 <param name="center" value="Some research center"/> | |
| 586 <output name="experiments_table_out"> | |
| 587 <assert_contents> | |
| 588 <has_n_lines n="2"/> | |
| 589 <has_n_columns n="17"/> | |
| 590 </assert_contents> | |
| 591 </output> | |
| 592 <output name="studies_table_out"> | |
| 593 <assert_contents> | |
| 594 <has_n_lines n="2"/> | |
| 595 <has_n_columns n="8"/> | |
| 596 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> | |
| 597 </assert_contents> | |
| 598 </output> | |
| 599 <output name="samples_table_out"> | |
| 600 <assert_contents> | |
| 601 <has_n_lines n="2"/> | |
| 602 <has_n_columns n="8"/> | |
| 603 </assert_contents> | |
| 604 </output> | |
| 605 <output name="runs_table_out"> | |
| 606 <assert_contents> | |
| 607 <has_n_lines n="3"/> | |
| 608 <has_n_columns n="8"/> | |
| 609 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/> | |
| 610 </assert_contents> | |
| 611 </output> | |
| 612 </test> | |
| 613 <!--Test 6: RUN failing build tables from user input fields NON-VIRAL samples--> | |
| 614 <test expect_failure="true"> | |
| 615 <conditional name="action_options"> | |
| 616 <param name="action" value="add"/> | |
| 617 <section name="test_submit_parameters"> | |
| 618 <param name="submit_dev" value="true" /> | |
| 619 <param name="dry_run" value="false" /> | |
| 620 </section> | |
| 621 <conditional name="input_format_conditional"> | |
| 622 <param name="input_format" value="build_tables"/> | |
| 623 <param name="add_extension" value="true"/> | |
| 624 <conditional name="conditional_viral_metadata"> | |
| 625 <param name="viral_sample" value="false"/> | |
| 626 <repeat name="rep_study"> | |
| 627 <param name="study_title" value="Test study title"/> | |
| 628 <param name="study_abstract" value="Test study abstract"/> | |
| 629 <param name="study_type" value="Epigenetics"/> | |
| 630 <param name="study_pubmed_id" value="Test study pubmedID"/> | |
| 631 <repeat name="rep_sample"> | |
| 632 <param name="sample_title" value="Test Sample title"/> | |
| 633 <param name="sample_description" value="Test Sample description"/> | |
| 634 <param name="scientific_name" value="Test Sample scientific name"/> | |
| 635 <param name="tax_id" value="Test Sample tax_id"/> | |
| 636 <repeat name="rep_experiment"> | |
| 637 <param name="experiment_title" value="Test experiment title"/> | |
| 638 <param name="experiment_design" value="Test experiment design description"/> | |
| 639 <param name="library_strategy" value="CTS"/> | |
| 640 <param name="library_source" value="GENOMIC"/> | |
| 641 <param name="library_selection" value="PCR"/> | |
| 642 <param name="library_layout" value="SINGLE"/> | |
| 643 <param name="insert_size" value="150"/> | |
| 644 <param name="library_construction_protocol" value="Test library construction"/> | |
| 645 <param name="platform" value="ILLUMINA"/> | |
| 646 <param name="instrument_model" value="Illumina HiSeq 4000"/> | |
| 647 <repeat name="rep_runs"> | |
| 648 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> | |
| 649 </repeat> | |
| 650 </repeat> | |
| 651 </repeat> | |
| 652 </repeat> | |
| 653 </conditional> | |
| 654 </conditional> | |
| 655 </conditional> | |
| 656 <param name="center" value="Some research center"/> | |
| 657 <assert_stdout> | |
| 658 <has_text_matching expression="No ENA credentials defined"/> | |
| 659 </assert_stdout> | |
| 660 </test> | |
| 661 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples | |
| 662 also tests compression of uncompressed inputs and adding the .gz suffix --> | |
| 663 <test expect_failure="true"> | |
| 664 <conditional name="action_options"> | |
| 665 <param name="action" value="add"/> | |
| 666 <section name="test_submit_parameters"> | |
| 667 <param name="submit_dev" value="true" /> | |
| 668 <param name="dry_run" value="false" /> | |
| 669 </section> | |
| 670 <param name="test_submit" value="True"/> | |
| 671 <conditional name="input_format_conditional"> | |
| 672 <param name="add_extension" value="true"/> | |
| 673 <param name="input_format" value="build_tables"/> | |
| 674 <conditional name="conditional_viral_metadata"> | |
| 675 <param name="viral_sample" value="false"/> | |
| 676 <repeat name="rep_study"> | |
| 677 <param name="study_title" value="Test study title"/> | |
| 678 <param name="study_abstract" value="Test study abstract"/> | |
| 679 <param name="study_type" value="Epigenetics"/> | |
| 680 <param name="study_pubmed_id" value="Test study pubmedID"/> | |
| 681 <repeat name="rep_sample"> | |
| 682 <param name="sample_title" value="Test Sample title"/> | |
| 683 <param name="sample_description" value="Test Sample description"/> | |
| 684 <param name="scientific_name" value="Test Sample scientific name"/> | |
| 685 <param name="tax_id" value="Test Sample tax_id"/> | |
| 686 <repeat name="rep_experiment"> | |
| 687 <param name="experiment_title" value="Test experiment title"/> | |
| 688 <param name="experiment_design" value="Test experiment design description"/> | |
| 689 <param name="library_strategy" value="CTS"/> | |
| 690 <param name="library_source" value="GENOMIC"/> | |
| 691 <param name="library_selection" value="PCR"/> | |
| 692 <param name="library_layout" value="SINGLE"/> | |
| 693 <param name="insert_size" value="150"/> | |
| 694 <param name="library_construction_protocol" value="Test library construction"/> | |
| 695 <param name="platform" value="ILLUMINA"/> | |
| 696 <param name="instrument_model" value="Illumina HiSeq 4000"/> | |
| 697 <repeat name="rep_runs"> | |
| 698 <param name="run_base_name" value="run_from_hospital_X"/> | |
| 699 <param name="upload_files" value="sample.fq,sample.fq" ftype="fastqsanger"/> | |
| 700 </repeat> | |
| 701 </repeat> | |
| 702 </repeat> | |
| 703 </repeat> | |
| 704 </conditional> | |
| 705 </conditional> | |
| 706 </conditional> | |
| 707 <param name="center" value="Some research center"/> | |
| 708 <assert_command> | |
| 709 <has_text_matching expression="ena-upload-cli"/> | |
| 710 <has_text_matching expression="--data 'sample.fq.fastq.gz' 'sample.fq.fastq.gz'"/> | |
| 711 <has_text_matching expression="--action 'add' --center 'Some research center'"/> | |
| 712 <not_has_text text="modify" /> | |
| 713 </assert_command> | |
| 714 <assert_stderr> | |
| 715 <has_text_matching expression="Oops, the file test_fake_path does not exist"/> | |
| 716 </assert_stderr> | |
| 717 </test> | |
| 718 <!--Test 8: viral submission - User input metadata - Add extension = False--> | |
| 719 <test expect_failure="true"> | |
| 720 <conditional name="action_options"> | |
| 721 <param name="action" value="add"/> | |
| 722 <section name="test_submit_parameters"> | |
| 723 <param name="submit_dev" value="false" /> | |
| 724 <param name="dry_run" value="false" /> | |
| 725 </section> | |
| 726 <param name="test_submit" value="True"/> | |
| 727 <conditional name="input_format_conditional"> | |
| 728 <param name="add_extension" value="False"/> | |
| 729 <param name="input_format" value="build_tables"/> | |
| 730 <conditional name="conditional_viral_metadata"> | |
| 731 <param name="viral_sample" value="true"/> | |
| 732 <repeat name="rep_study"> | |
| 733 <param name="study_title" value="Test study title"/> | |
| 734 <param name="study_abstract" value="Test study abstract"/> | |
| 735 <param name="study_type" value="Epigenetics"/> | |
| 736 <param name="study_pubmed_id" value="Test study pubmedID"/> | |
| 737 <repeat name="rep_sample"> | |
| 738 <param name="sample_title" value="Test Sample title"/> | |
| 739 <param name="sample_description" value="Test Sample description"/> | |
| 740 <param name="scientific_name" value="Test Sample scientific name"/> | |
| 741 <param name="tax_id" value="Test Sample tax_id"/> | |
| 742 <param name="collection_date" value="2020"/> | |
| 743 <param name="geo_location_country" value="Belgium"/> | |
| 744 <param name="host_common_name" value="Human"/> | |
| 745 <param name="host_subject_id" value="Patient_001"/> | |
| 746 <param name="host_health_state" value="healthy"/> | |
| 747 <param name="host_sex" value="female"/> | |
| 748 <param name="host_scientific_name" value="homo sapiens"/> | |
| 749 <param name="collector_name" value="John The Collector"/> | |
| 750 <param name="collecting_institution" value="Hospital 01"/> | |
| 751 <param name="isolate" value="sample_001"/> | |
| 752 <repeat name="rep_experiment"> | |
| 753 <param name="experiment_title" value="Test experiment title"/> | |
| 754 <param name="experiment_design" value="Test experiment design description"/> | |
| 755 <param name="library_strategy" value="CTS"/> | |
| 756 <param name="library_source" value="GENOMIC"/> | |
| 757 <param name="library_selection" value="PCR"/> | |
| 758 <param name="library_layout" value="SINGLE"/> | |
| 759 <param name="insert_size" value="150"/> | |
| 760 <param name="library_construction_protocol" value="Test library construction"/> | |
| 761 <param name="platform" value="ILLUMINA"/> | |
| 762 <param name="instrument_model" value="Illumina HiSeq 4000"/> | |
| 763 <repeat name="rep_runs"> | |
| 764 <param name="run_base_name" value="run_from_hospital_X"/> | |
| 765 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/> | |
| 766 </repeat> | |
| 767 </repeat> | |
| 768 </repeat> | |
| 769 </repeat> | |
| 770 </conditional> | |
| 771 </conditional> | |
| 772 </conditional> | |
| 773 <param name="center" value="Some research center"/> | |
| 774 <assert_command> | |
| 775 <has_text_matching expression="ena-upload-cli"/> | |
| 776 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> | |
| 777 <has_text_matching expression="--action 'add' --center 'Some research center'"/> | |
| 778 <has_text_matching expression="--checklist ERC000033"/> | |
| 779 </assert_command> | |
| 780 <assert_stderr> | |
| 781 <has_text_matching expression="Oops, the file test_fake_path does not exist"/> | |
| 782 </assert_stderr> | |
| 783 </test> | |
| 784 <!--Test 9: modify option and auto compression - viral submission - User input metadata--> | |
| 785 <test expect_failure="true"> | |
| 786 <conditional name="action_options"> | |
| 787 <param name="action" value="modify"/> | |
| 788 <section name="test_submit_parameters"> | |
| 789 <param name="submit_dev" value="false" /> | |
| 790 <param name="dry_run" value="false" /> | |
| 791 </section> | |
| 792 <param name="test_submit" value="True"/> | |
| 793 <conditional name="input_format_conditional"> | |
| 794 <param name="add_extension" value="False"/> | |
| 795 <param name="input_format" value="build_tables"/> | |
| 796 <conditional name="conditional_viral_metadata"> | |
| 797 <param name="viral_sample" value="True"/> | |
| 798 <repeat name="rep_study"> | |
| 799 <param name="study_title" value="Test study title"/> | |
| 800 <param name="study_abstract" value="Test study abstract"/> | |
| 801 <param name="study_type" value="Epigenetics"/> | |
| 802 <param name="study_pubmed_id" value="Test study pubmedID"/> | |
| 803 <repeat name="rep_sample"> | |
| 804 <param name="sample_title" value="Test Sample title"/> | |
| 805 <param name="sample_description" value="Test Sample description"/> | |
| 806 <param name="scientific_name" value="Test Sample scientific name"/> | |
| 807 <param name="tax_id" value="Test Sample tax_id"/> | |
| 808 <param name="collection_date" value="2020"/> | |
| 809 <param name="geo_location_country" value="Belgium"/> | |
| 810 <param name="host_common_name" value="Human"/> | |
| 811 <param name="host_subject_id" value="Patient_001"/> | |
| 812 <param name="host_health_state" value="healthy"/> | |
| 813 <param name="host_sex" value="female"/> | |
| 814 <param name="host_scientific_name" value="homo sapiens"/> | |
| 815 <param name="collector_name" value="John The Collector"/> | |
| 816 <param name="collecting_institution" value="Hospital 01"/> | |
| 817 <param name="isolate" value="sample_001"/> | |
| 818 <repeat name="rep_experiment"> | |
| 819 <param name="experiment_title" value="Test experiment title"/> | |
| 820 <param name="experiment_design" value="Test experiment design description"/> | |
| 821 <param name="library_strategy" value="CTS"/> | |
| 822 <param name="library_source" value="GENOMIC"/> | |
| 823 <param name="library_selection" value="PCR"/> | |
| 824 <param name="library_layout" value="SINGLE"/> | |
| 825 <param name="insert_size" value="150"/> | |
| 826 <param name="library_construction_protocol" value="Test library construction"/> | |
| 827 <param name="platform" value="ILLUMINA"/> | |
| 828 <param name="instrument_model" value="Illumina HiSeq 4000"/> | |
| 829 <repeat name="rep_runs"> | |
| 830 <param name="run_base_name" value="run_from_hospital_X"/> | |
| 831 <param name="upload_files" value="sample.fq" ftype="fastqsanger"/> | |
| 832 </repeat> | |
| 833 </repeat> | |
| 834 </repeat> | |
| 835 </repeat> | |
| 836 </conditional> | |
| 837 </conditional> | |
| 838 </conditional> | |
| 839 <param name="center" value="Some research center"/> | |
| 840 <assert_command> | |
| 841 <has_text_matching expression="ena-upload-cli"/> | |
| 842 <has_text_matching expression="--data 'sample.fq.gz'"/> | |
| 843 <has_text_matching expression="--action 'modify' --center 'Some research center'"/> | |
| 844 <has_text_matching expression="--checklist ERC000033"/> | |
| 845 <not_has_text text="add" /> | |
| 846 </assert_command> | |
| 847 <assert_stderr> | |
| 848 <has_text_matching expression="Oops, the file test_fake_path does not exist"/> | |
| 849 </assert_stderr> | |
| 850 </test> | |
| 851 </tests> | |
| 852 <help><![CDATA[ | |
| 853 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli | |
| 854 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 | |
| 855 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 | |
| 856 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 | |
| 857 ]]></help> | |
| 858 <citations> | |
| 859 </citations> | |
| 860 </tool> |