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comparison ena_upload.xml @ 1:57251c760cab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
author iuc
date Fri, 30 Apr 2021 12:09:25 +0000
parents 382518f24d6d
children 9e2df763086c
comparison
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0:382518f24d6d 1:57251c760cab
1 <tool id="ena_upload" name="ENA Upload tool" version="0.3" profile="20.01" license="MIT"> 1 <tool id="ena_upload" name="ENA Upload tool" version="0.3.1" profile="20.01" license="MIT">
2 <macros> 2 <macros>
3 <token name="@VERSION@">0.2.4</token> 3 <token name="@VERSION@">0.2.7</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> 8 <requirement type="package" version="1.2.0">xlrd</requirement>
9 </requirements> 9 </requirements>
10 <stdio>
11 <regex match="Oops" source="stderr" level="fatal"/>
12 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
13 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
11 mkdir ./submission_files; 15 mkdir ./submission_files;
16 #set $studies_table_path = './submission_files/studies.tsv'
17 #set $samples_table_path = './submission_files/samples.tsv'
18 #set $experiments_table_path = './submission_files/experiments.tsv'
19 #set $runs_table_path = './submission_files/runs.tsv'
20
21 #set $studies_table_path_updated = './submission_files/studies_updated.tsv'
22 #set $samples_table_path_updated = './submission_files/samples_updated.tsv'
23 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv'
24 #set $runs_table_path_updated = './submission_files/runs_updated.tsv'
12 25
13 #set working_dir = os.getcwd() 26 #set working_dir = os.getcwd()
14 #set $dry_run_option = "False"
15 #set viral_submission = "False"
16 #if $action_options.input_format_conditional.input_format == "build_tables": 27 #if $action_options.input_format_conditional.input_format == "build_tables":
17 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json; 28 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
18 #set $studies_table_path = './submission_files/studies.tsv'
19 #set $samples_table_path = './submission_files/samples.tsv'
20 #set $experiments_table_path = './submission_files/experiments.tsv'
21 #set $runs_table_path = './submission_files/runs.tsv'
22 #end if 29 #end if
23 30
24 #if $action_options.input_format_conditional.input_format == "excel_tables": 31 #if $action_options.input_format_conditional.input_format == "excel_tables":
25 python '$__tool_directory__/process_xlsx.py' 32 python '$__tool_directory__/process_xlsx.py'
26 #if $action_options.input_format_conditional.viral_submission == "true": 33 #if $action_options.input_format_conditional.viral_submission == "true":
27 --vir 34 --vir
28 #end if 35 #end if
29 --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files ; 36 --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files --verbose > '$output';
30 #set $studies_table_path = './submission_files/studies.tsv'
31 #set $samples_table_path = './submission_files/samples.tsv'
32 #set $experiments_table_path = './submission_files/experiments.tsv'
33 #set $runs_table_path = './submission_files/runs.tsv'
34 #if $action_options.input_format_conditional.dry_run == "true":
35 #set $dry_run_option = "True"
36 #end if
37 #end if 37 #end if
38 38
39 #if $action_options.input_format_conditional.input_format != "user_generated_tables": 39 #if $action_options.input_format_conditional.input_format != "user_generated_tables":
40 cp $studies_table_path $studies_table_out; 40 cp $studies_table_path $studies_table_out &&
41 cp $samples_table_path $samples_table_out; 41 cp $samples_table_path $samples_table_out &&
42 cp $experiments_table_path $experiments_table_out; 42 cp $experiments_table_path $experiments_table_out &&
43 cp $runs_table_path $runs_table_out; 43 cp $runs_table_path $runs_table_out &&
44 #if $action_options.input_format_conditional.dry_run == "true": 44 #else:
45 #set $dry_run_option = "True" 45 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
46 #end if 46 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
47 #end if 47 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
48 48 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
49 49 #end if
50 #if $dry_run_option == "False" and $action_options.test_submit == "False": 50
51
52 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
51 webin_id=`grep 'username' $credentials`; 53 webin_id=`grep 'username' $credentials`;
52 if [ "\$webin_id" = "" ]; then 54 if [ "\$webin_id" = "" ]; then
53 ## No credentials in user defined preferences 55 ## No credentials in user defined preferences
54 ## Fallback to global defined credentials (if exist) 56 ## Fallback to global defined credentials (if exist)
55 #import os 57 #import os
56 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): 58 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
57 credentials_path=\${ENA_SECRETS}; 59 credentials_path=\${GALAXY_ENA_SECRETS};
58 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`; 60 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
59 if [ "\$webin_id" = "" ]; then 61 if [ "\$webin_id" = "" ]; then
60 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information"; 62 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
61 exit 1; 63 exit 1;
62 fi; 64 fi;
89 #end for 91 #end for
90 #end for 92 #end for
91 #end for 93 #end for
92 #end for 94 #end for
93 #else: 95 #else:
94 #for $file in $action_options.input_format_conditional.data: 96 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list':
95 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) 97 #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection:
96 ln -s '$file' $safename_reads_file && 98 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
97 $files_to_upload.append(str($safename_reads_file)) 99 #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
98 #end for 100 #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq.gz'
99 #end if 101 #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
100 102 #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq.bz2'
101 103 #else:
102 #if $dry_run_option == "False": 104 #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq'
105 #end if
106 #if $pair.reverse.is_of_type('fastq.gz', 'fastqsanger.gz'):
107 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq.gz'
108 #elif $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
109 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq.bz2'
110 #else:
111 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq'
112 #end if
113
114 ln -s '$pair.forward' $safename_fwd_reads_file &&
115 $files_to_upload.append(str($safename_fwd_reads_file))
116 ln -s '$pair.reverse' $safename_rev_reads_file &&
117 $files_to_upload.append(str($safename_rev_reads_file))
118 #end for
119 #end if
120 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
121 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
122 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
123 ln -s '$file' $safename_reads_file &&
124 $files_to_upload.append(str($safename_reads_file))
125 #end for
126 #end if
127 #end if
128
129
130 #if $action_options.test_submit_parameters.dry_run == "false":
103 ena-upload-cli 131 ena-upload-cli
104 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' 132 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
105 --action '$action_options.action' 133 --action '$action_options.action'
106 --center '$action_options.center' 134 --center '$action_options.center'
107 --secret \${credentials_path} 135 --secret \${credentials_path}
108 --data 136 --data
109 #for $dataset in $files_to_upload: 137 #for $dataset in $files_to_upload:
110 '$dataset' 138 '$dataset'
111 #end for 139 #end for
140 --experiment '$experiments_table_path'
141 --study '$studies_table_path'
142 --run '$runs_table_path'
143 --sample '$samples_table_path'
112 #if $action_options.input_format_conditional.input_format == "user_generated_tables": 144 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
113 --experiment '$action_options.input_format_conditional.experiments_users_table'
114 --study '$action_options.input_format_conditional.studies_users_table'
115 --run '$action_options.input_format_conditional.runs_users_table'
116 --sample '$action_options.input_format_conditional.samples_users_table'
117 #if "$action_options.input_format_conditional.viral_submission" == "true": 145 #if "$action_options.input_format_conditional.viral_submission" == "true":
118 --vir 146 --vir
119 #end if 147 #end if
120 #else: 148 #else:
121 --experiment '$experiments_table_path'
122 --study '$studies_table_path'
123 --run '$runs_table_path'
124 --sample '$samples_table_path'
125 #if $action_options.input_format_conditional.input_format == "build_tables": 149 #if $action_options.input_format_conditional.input_format == "build_tables":
126 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": 150 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
127 --vir 151 --vir
128 #end if 152 #end if
129 #else: 153 #else:
131 --vir 155 --vir
132 #end if 156 #end if
133 #end if 157 #end if
134 #end if 158 #end if
135 159
136 #if $action_options.submit_dev == "true": 160 #if $action_options.test_submit_parameters.submit_dev == "true":
137 -d 161 -d
138 #end if 162 #end if
139 > '$output' 163 >> '$output';
164 echo -e 'center_name\t$action_options.center' >> '$output';
165 echo -e 'action_option\t$action_options.action' >> '$output';
166 #if $action_options.input_format_conditional.input_format != "user_generated_tables":
167 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
168 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
169 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
170 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
171 #end if
140 #else: 172 #else:
141 echo ""
142 exit 0; 173 exit 0;
143 #end if 174 #end if
144 175
145 ]]></command> 176 ]]></command>
146 <configfiles> 177 <configfiles>
168 #set run_files = list() 199 #set run_files = list()
169 #for $file in $run.upload_files: 200 #for $file in $run.upload_files:
170 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) 201 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
171 $run_files.append(str($safename_reads_file)) 202 $run_files.append(str($safename_reads_file))
172 #end for 203 #end for
173 $runs.append($run_files) 204 $runs.append((str($run.run_base_name),$run_files))
174 #end for 205 #end for
175 206
176 $experiments.append({'title':str($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}) 207 $experiments.append({'title':str($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})
177 #end for 208 #end for
178 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": 209 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
179 210
180 $samples.append({'title':str($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}) 211 $samples.append({'title':str($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})
194 <param name="action" type="select" label="Action to execute"> 225 <param name="action" type="select" label="Action to execute">
195 <option value="add" selected="True">Add new data</option> 226 <option value="add" selected="True">Add new data</option>
196 <option value="modify">Modify metadata</option> 227 <option value="modify">Modify metadata</option>
197 </param> 228 </param>
198 <when value="add"> 229 <when value="add">
199 <param name="submit_dev" type="boolean" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted " /> 230 <expand macro="test_submit_section"/>
200 <param name="test_submit" type="hidden" value="False" /> 231 <param name="test_submit" type="hidden" value="False" />
201 <expand macro="table_inputs_macro" /> 232 <expand macro="table_inputs_macro" />
202 </when> 233 </when>
203 <when value="modify"> 234 <when value="modify">
235 <expand macro="test_submit_section"/>
204 <expand macro="table_inputs_macro" /> 236 <expand macro="table_inputs_macro" />
205 </when> 237 </when>
206 </conditional> 238 </conditional>
207 </inputs> 239 </inputs>
208 <outputs> 240 <outputs>
209 <data name="output" format="data" label="${tool.name} on ${on_string}: Upload summary"/> 241 <data name="output" format="txt" label="ENA submission receipt"/>
210 <data name="studies_table_out" format="tabular" label="Studies table"> 242 <data name="studies_table_out" format="tabular" label="Studies table">
211 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 243 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
212 </data> 244 </data>
213 <data name="samples_table_out" format="tabular" label="Samples table"> 245 <data name="samples_table_out" format="tabular" label="Samples table">
214 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> 246 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
223 <tests> 255 <tests>
224 <!--Test excel input of VIRAL samples --> 256 <!--Test excel input of VIRAL samples -->
225 <test> 257 <test>
226 <conditional name="action_options"> 258 <conditional name="action_options">
227 <param name="action" value="add"/> 259 <param name="action" value="add"/>
228 <param name="submit_dev" value="False"/> 260 <section name="test_submit_parameters">
261 <param name="submit_dev" value="false" />
262 <param name="dry_run" value="true" />
263 </section>
229 <conditional name="input_format_conditional"> 264 <conditional name="input_format_conditional">
230 <param name="input_format" value="excel_tables"/> 265 <param name="input_format" value="excel_tables"/>
231 <param name="viral_submission" value="True"/> 266 <param name="viral_submission" value="True"/>
232 <param name="dry_run" value="True"/>
233 <param name="xlsx_file" value="metadata_test_viral.xlsx"/> 267 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
234 <param name="data" value="sample.fq"/> 268 <conditional name="run_input_format_conditional">
269 <param name="run_input_format" value="multiple_selection_list"/>
270 <param name="data" value="sample.fq"/>
271 </conditional>
235 </conditional> 272 </conditional>
236 </conditional> 273 </conditional>
237 <param name="center" value="Some research center"/> 274 <param name="center" value="Some research center"/>
238 <output name="experiments_table_out"> 275 <output name="experiments_table_out">
239 <assert_contents> 276 <assert_contents>
269 </test> 306 </test>
270 <!--Test excel input of NON-VIRAL samples--> 307 <!--Test excel input of NON-VIRAL samples-->
271 <test> 308 <test>
272 <conditional name="action_options"> 309 <conditional name="action_options">
273 <param name="action" value="add"/> 310 <param name="action" value="add"/>
274 <param name="submit_dev" value="False"/> 311 <section name="test_submit_parameters">
312 <param name="submit_dev" value="false" />
313 <param name="dry_run" value="true" />
314 </section>
275 <conditional name="input_format_conditional"> 315 <conditional name="input_format_conditional">
276 <param name="input_format" value="excel_tables"/> 316 <param name="input_format" value="excel_tables"/>
277 <param name="viral_submission" value="False"/> 317 <param name="viral_submission" value="False"/>
278 <param name="dry_run" value="True"/>
279 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> 318 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
280 <param name="data" value="sample.fq"/> 319 <conditional name="run_input_format_conditional">
320 <param name="run_input_format" value="multiple_selection_list"/>
321 <param name="data" value="sample.fq"/>
322 </conditional>
281 </conditional> 323 </conditional>
282 </conditional> 324 </conditional>
283 <param name="center" value="Some research center"/> 325 <param name="center" value="Some research center"/>
284 <output name="experiments_table_out"> 326 <output name="experiments_table_out">
285 <assert_contents> 327 <assert_contents>
308 <has_n_columns n="8"/> 350 <has_n_columns n="8"/>
309 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/> 351 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
310 <has_line_matching expression="r_(.*)_026\tadd\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/> 352 <has_line_matching expression="r_(.*)_026\tadd\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/>
311 </assert_contents> 353 </assert_contents>
312 </output> 354 </output>
355 </test>
356 <!--Test failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
357 <test expect_failure="true">
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="false" />
363 </section>
364 <conditional name="input_format_conditional">
365 <param name="input_format" value="excel_tables"/>
366 <param name="viral_submission" value="False"/>
367 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
368 <conditional name="run_input_format_conditional">
369 <param name="run_input_format" value="paired_list"/>
370 <param name="paired_end_collection">
371 <collection type="list:paired">
372 <element name="paired_run_name">
373 <collection type="paired">
374 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" />
375 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" />
376 </collection>
377 </element>
378 </collection>
379 </param>
380 </conditional>
381 </conditional>
382 </conditional>
383 <param name="center" value="Some research center"/>
384 <assert_command>
385 <has_text_matching expression="ena-upload-cli"/>
386 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
387 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
388 </assert_command>
313 </test> 389 </test>
314 <!--Test build tables from user input fields NON-VIRAL samples--> 390 <!--Test build tables from user input fields NON-VIRAL samples-->
315 <test> 391 <test>
316 <conditional name="action_options"> 392 <conditional name="action_options">
317 <param name="action" value="add"/> 393 <param name="action" value="add"/>
318 <param name="submit_dev" value="False"/> 394 <section name="test_submit_parameters">
395 <param name="submit_dev" value="false" />
396 <param name="dry_run" value="true" />
397 </section>
319 <conditional name="input_format_conditional"> 398 <conditional name="input_format_conditional">
320 <param name="input_format" value="build_tables"/> 399 <param name="input_format" value="build_tables"/>
321 <param name="dry_run" value="True"/>
322 <conditional name="conditional_viral_metadata"> 400 <conditional name="conditional_viral_metadata">
323 <param name="viral_sample" value="False"/> 401 <param name="viral_sample" value="False"/>
324 <repeat name="rep_study"> 402 <repeat name="rep_study">
325 <param name="study_title" value="Test study title"/> 403 <param name="study_title" value="Test study title"/>
326 <param name="study_abstract" value="Test study abstract"/> 404 <param name="study_abstract" value="Test study abstract"/>
381 </test> 459 </test>
382 <!--Test RUN failing build tables from user input fields NON-VIRAL samples--> 460 <!--Test RUN failing build tables from user input fields NON-VIRAL samples-->
383 <test expect_failure="true"> 461 <test expect_failure="true">
384 <conditional name="action_options"> 462 <conditional name="action_options">
385 <param name="action" value="add"/> 463 <param name="action" value="add"/>
386 <param name="submit_dev" value="True"/> 464 <section name="test_submit_parameters">
465 <param name="submit_dev" value="true" />
466 <param name="dry_run" value="false" />
467 </section>
387 <conditional name="input_format_conditional"> 468 <conditional name="input_format_conditional">
388 <param name="input_format" value="build_tables"/> 469 <param name="input_format" value="build_tables"/>
389 <param name="dry_run" value="False"/>
390 <conditional name="conditional_viral_metadata"> 470 <conditional name="conditional_viral_metadata">
391 <param name="viral_sample" value="False"/> 471 <param name="viral_sample" value="false"/>
392 <repeat name="rep_study"> 472 <repeat name="rep_study">
393 <param name="study_title" value="Test study title"/> 473 <param name="study_title" value="Test study title"/>
394 <param name="study_abstract" value="Test study abstract"/> 474 <param name="study_abstract" value="Test study abstract"/>
395 <param name="study_type" value="Epigenetics"/> 475 <param name="study_type" value="Epigenetics"/>
396 <param name="study_pubmed_id" value="Test study pubmedID"/> 476 <param name="study_pubmed_id" value="Test study pubmedID"/>
426 </test> 506 </test>
427 <!--Test with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples--> 507 <!--Test with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples-->
428 <test expect_failure="true"> 508 <test expect_failure="true">
429 <conditional name="action_options"> 509 <conditional name="action_options">
430 <param name="action" value="add"/> 510 <param name="action" value="add"/>
431 <param name="submit_dev" value="True"/> 511 <section name="test_submit_parameters">
512 <param name="submit_dev" value="true" />
513 <param name="dry_run" value="false" />
514 </section>
432 <param name="test_submit" value="True"/> 515 <param name="test_submit" value="True"/>
433 <conditional name="input_format_conditional"> 516 <conditional name="input_format_conditional">
434 <param name="input_format" value="build_tables"/> 517 <param name="input_format" value="build_tables"/>
435 <param name="dry_run" value="False"/>
436 <conditional name="conditional_viral_metadata"> 518 <conditional name="conditional_viral_metadata">
437 <param name="viral_sample" value="False"/> 519 <param name="viral_sample" value="false"/>
438 <repeat name="rep_study"> 520 <repeat name="rep_study">
439 <param name="study_title" value="Test study title"/> 521 <param name="study_title" value="Test study title"/>
440 <param name="study_abstract" value="Test study abstract"/> 522 <param name="study_abstract" value="Test study abstract"/>
441 <param name="study_type" value="Epigenetics"/> 523 <param name="study_type" value="Epigenetics"/>
442 <param name="study_pubmed_id" value="Test study pubmedID"/> 524 <param name="study_pubmed_id" value="Test study pubmedID"/>
455 <param name="insert_size" value="150"/> 537 <param name="insert_size" value="150"/>
456 <param name="library_construction_protocol" value="Test library construction"/> 538 <param name="library_construction_protocol" value="Test library construction"/>
457 <param name="platform" value="ILLUMINA"/> 539 <param name="platform" value="ILLUMINA"/>
458 <param name="instrument_model" value="Illumina HiSeq 4000"/> 540 <param name="instrument_model" value="Illumina HiSeq 4000"/>
459 <repeat name="rep_runs"> 541 <repeat name="rep_runs">
542 <param name="run_base_name" value="run_from_hospital_X"/>
460 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> 543 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
461 </repeat> 544 </repeat>
462 </repeat> 545 </repeat>
463 </repeat> 546 </repeat>
464 </repeat> 547 </repeat>
470 <has_text_matching expression="ena-upload-cli"/> 553 <has_text_matching expression="ena-upload-cli"/>
471 <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/> 554 <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/>
472 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 555 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
473 </assert_command> 556 </assert_command>
474 <assert_stderr> 557 <assert_stderr>
475 <has_text_matching expression="ENA_upload: error: Oops, the file test_fake_path does not exist"/> 558 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
476 </assert_stderr> 559 </assert_stderr>
477 </test> 560 </test>
478 <!--test viral submission - User input metadata--> 561 <!--test viral submission - User input metadata-->
479 <test expect_failure="true"> 562 <test expect_failure="true">
480 <conditional name="action_options"> 563 <conditional name="action_options">
481 <param name="action" value="add"/> 564 <param name="action" value="add"/>
482 <param name="submit_dev" value="False"/> 565 <section name="test_submit_parameters">
566 <param name="submit_dev" value="false" />
567 <param name="dry_run" value="false" />
568 </section>
483 <param name="test_submit" value="True"/> 569 <param name="test_submit" value="True"/>
484 <conditional name="input_format_conditional"> 570 <conditional name="input_format_conditional">
485 <param name="input_format" value="build_tables"/> 571 <param name="input_format" value="build_tables"/>
486 <param name="dry_run" value="False"/>
487 <conditional name="conditional_viral_metadata"> 572 <conditional name="conditional_viral_metadata">
488 <param name="viral_sample" value="True"/> 573 <param name="viral_sample" value="True"/>
489 <repeat name="rep_study"> 574 <repeat name="rep_study">
490 <param name="study_title" value="Test study title"/> 575 <param name="study_title" value="Test study title"/>
491 <param name="study_abstract" value="Test study abstract"/> 576 <param name="study_abstract" value="Test study abstract"/>
516 <param name="insert_size" value="150"/> 601 <param name="insert_size" value="150"/>
517 <param name="library_construction_protocol" value="Test library construction"/> 602 <param name="library_construction_protocol" value="Test library construction"/>
518 <param name="platform" value="ILLUMINA"/> 603 <param name="platform" value="ILLUMINA"/>
519 <param name="instrument_model" value="Illumina HiSeq 4000"/> 604 <param name="instrument_model" value="Illumina HiSeq 4000"/>
520 <repeat name="rep_runs"> 605 <repeat name="rep_runs">
606 <param name="run_base_name" value="run_from_hospital_X"/>
521 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> 607 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
522 </repeat> 608 </repeat>
523 </repeat> 609 </repeat>
524 </repeat> 610 </repeat>
525 </repeat> 611 </repeat>
532 <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/> 618 <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/>
533 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 619 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
534 <has_text_matching expression="--vir"/> 620 <has_text_matching expression="--vir"/>
535 </assert_command> 621 </assert_command>
536 <assert_stderr> 622 <assert_stderr>
537 <has_text_matching expression="ENA_upload: error: Oops, the file test_fake_path does not exist"/> 623 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
538 </assert_stderr> 624 </assert_stderr>
539 </test> 625 </test>
540 </tests> 626 </tests>
541 <help><![CDATA[ 627 <help><![CDATA[
542 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli 628 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli