Mercurial > repos > ieguinoa > ena_upload

comparison ena_upload.xml @ 2:2f7a70c0d3ab draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ieguinoa
date Mon, 21 Feb 2022 14:22:53 +0000
parents 5d59238cd3f4
children
comparison
equal deleted inserted replaced
1:9681a9180730 2:2f7a70c0d3ab
24 24
25 #set working_dir = os.getcwd() 25 #set working_dir = os.getcwd()
26 #if $action_options.input_format_conditional.input_format == "build_tables": 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 $studies_json; 27 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
28 #end if 28 #end if
29
30 credentials_path='test_fake_path';
31 echo "username: test_user" > \$credentials_path;
32 echo "password: test_password" >> \$credentials_path;
29 33
30 34
31 #if $action_options.input_format_conditional.input_format == "build_tables": 35 #if $action_options.input_format_conditional.input_format == "build_tables":
32 cp $studies_table_path $studies_table_out && 36 cp $studies_table_path $studies_table_out &&
33 cp $samples_table_path $samples_table_out && 37 cp $samples_table_path $samples_table_out &&
63 else 67 else
64 credentials_path='$credentials'; 68 credentials_path='$credentials';
65 fi; 69 fi;
66 #end if 70 #end if
67 71
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 72
76 ## create the list of files to upload and make the symlinks 73 ## create the list of files to upload and make the symlinks
77 #import re 74 #import re
78 #set $files_to_upload = list() 75 #set $files_to_upload = list()
79 #if $action_options.input_format_conditional.input_format == "build_tables": 76 #if $action_options.input_format_conditional.input_format == "build_tables":
171 $files_to_upload.append(str($safename_reads_file)) 168 $files_to_upload.append(str($safename_reads_file))
172 #end for 169 #end for
173 #end if 170 #end if
174 #end if 171 #end if
175 172
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": 173 #if $action_options.action == "add":
179 ena-upload-cli 174 ena-upload-cli
180 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' 175 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
181 --action '$action_options.action' 176 --action '$action_options.action'
182 --center '$action_options.center' 177 --center '$action_options.center'
213 -d 208 -d
214 #end if 209 #end if
215 >> '$output'; 210 >> '$output';
216 #end if 211 #end if
217 212
213
214
218 #if $action_options.action == "modify": 215 #if $action_options.action == "modify":
219 ena-upload-cli 216 ena-upload-cli
220 --tool 'ena-upload-cli v@VERSION@ @ Galaxy' 217 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
221 --action '$action_options.action' 218 --action '$action_options.action'
222 --center '$action_options.center' 219 --center '$action_options.center'
249 --checklist $action_options.input_format_conditional.checklist_id 246 --checklist $action_options.input_format_conditional.checklist_id
250 #end if 247 #end if
251 #end if 248 #end if
252 >> '$output'; 249 >> '$output';
253 #end if 250 #end if
254 #if $action_options.test_submit_parameters.dry_run == "false": 251
255 echo -e 'center_name\t$action_options.center' >> '$output'; 252 #if $action_options.test_submit_parameters.dry_run == "false":
256 echo -e 'action_option\t$action_options.action' >> '$output'; 253 echo -e 'center_name\t$action_options.center' >> '$output';
257 #if $action_options.input_format_conditional.input_format == "build_tables": 254 echo -e 'action_option\t$action_options.action' >> '$output';
258 cp $studies_table_path_updated $studies_table_out 2>/dev/null; 255 #end if
259 cp $samples_table_path_updated $samples_table_out 2>/dev/null; 256
260 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null; 257 ## copy updated files
261 cp $runs_table_path_updated $runs_table_out 2>/dev/null; 258 #if $action_options.input_format_conditional.input_format == "excel_tables":
262 #end if 259 ## for the excel input case, copy the upload-cli generated tables to the output files
263 #else 260 ## this applies for both draft and real submissions
264 ## for the excel input case, copy the upload-cli generated tables to the output files 261 cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
265 ## this applies for both draft and real submissions 262 cp './ENA_template_sample_updated.tsv' $samples_table_out;
266 cp './ENA_template_experiment_updated.tsv' $experiments_table_out; 263 cp './ENA_template_study_updated.tsv' $studies_table_out;
267 cp './ENA_template_sample_updated.tsv' $samples_table_out; 264 cp './ENA_template_run_updated.tsv' $runs_table_out;
268 cp './ENA_template_study_updated.tsv' $studies_table_out; 265 #else
269 cp './ENA_template_run_updated.tsv' $runs_table_out; 266 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
270 #end if 267 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
271 #else: 268 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
272 exit 0; 269 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
273 #end if 270 #end if
274 271
272 python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output;
275 ]]></command> 273 ]]></command>
276 <configfiles> 274 <configfiles>
277 <configfile name="credentials"><![CDATA[ 275 <configfile name="credentials"><![CDATA[
278 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip() 276 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
279 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip() 277 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
451 <has_n_columns n="8"/> 449 <has_n_columns n="8"/>
452 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> 450 <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(.*)"/> 451 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
454 </assert_contents> 452 </assert_contents>
455 </output> 453 </output>
454 <output name="output">
455 <assert_contents>
456 <has_line_matching expression="YAML -------------"/>
457 <has_line_matching expression="ENA_experiment:"/>
458 <has_line_matching expression="ENA_sample:"/>
459 <has_line_matching expression="ENA_study:"/>
460 <has_line_matching expression="ENA_run:"/>
461 </assert_contents>
462 </output>
456 </test> 463 </test>
457 <!--Test 3: excel input of NON-VIRAL samples--> 464 <!--Test 3: excel input of NON-VIRAL samples-->
458 <test> 465 <test>
459 <conditional name="action_options"> 466 <conditional name="action_options">
460 <param name="action" value="add"/> 467 <param name="action" value="add"/>
547 <param name="submit_dev" value="false" /> 554 <param name="submit_dev" value="false" />
548 <param name="dry_run" value="true" /> 555 <param name="dry_run" value="true" />
549 </section> 556 </section>
550 <conditional name="input_format_conditional"> 557 <conditional name="input_format_conditional">
551 <param name="input_format" value="build_tables"/> 558 <param name="input_format" value="build_tables"/>
552 <param name="add_extension" value="true"/> 559 <param name="add_extension" value="false"/>
553 <conditional name="conditional_viral_metadata"> 560 <conditional name="conditional_viral_metadata">
554 <param name="viral_sample" value="False"/> 561 <param name="viral_sample" value="False"/>
555 <repeat name="rep_study"> 562 <repeat name="rep_study">
556 <param name="study_title" value="Test study title"/> 563 <param name="study_title" value="Test study title"/>
557 <param name="study_abstract" value="Test study abstract"/> 564 <param name="study_abstract" value="Test study abstract"/>
559 <param name="study_pubmed_id" value="Test study pubmedID"/> 566 <param name="study_pubmed_id" value="Test study pubmedID"/>
560 <repeat name="rep_sample"> 567 <repeat name="rep_sample">
561 <param name="sample_title" value="Test Sample title"/> 568 <param name="sample_title" value="Test Sample title"/>
562 <param name="sample_description" value="Test Sample description"/> 569 <param name="sample_description" value="Test Sample description"/>
563 <param name="scientific_name" value="Test Sample scientific name"/> 570 <param name="scientific_name" value="Test Sample scientific name"/>
564 <param name="tax_id" value="Test Sample tax_id"/> 571 <param name="tax_id" value="2697049"/>
565 <repeat name="rep_experiment"> 572 <repeat name="rep_experiment">
566 <param name="experiment_title" value="Test experiment title"/> 573 <param name="experiment_title" value="Test experiment title"/>
567 <param name="experiment_design" value="Test experiment design description"/> 574 <param name="experiment_design" value="Test experiment design description"/>
568 <param name="library_strategy" value="CTS"/> 575 <param name="library_strategy" value="CTS"/>
569 <param name="library_source" value="GENOMIC"/> 576 <param name="library_source" value="GENOMIC"/>
572 <param name="insert_size" value="150"/> 579 <param name="insert_size" value="150"/>
573 <param name="library_construction_protocol" value="Test library construction"/> 580 <param name="library_construction_protocol" value="Test library construction"/>
574 <param name="platform" value="ILLUMINA"/> 581 <param name="platform" value="ILLUMINA"/>
575 <param name="instrument_model" value="Illumina HiSeq 4000"/> 582 <param name="instrument_model" value="Illumina HiSeq 4000"/>
576 <repeat name="rep_runs"> 583 <repeat name="rep_runs">
577 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> 584 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger.gz"/>
578 </repeat> 585 </repeat>
579 </repeat> 586 </repeat>
580 </repeat> 587 </repeat>
581 </repeat> 588 </repeat>
582 </conditional> 589 </conditional>
630 <param name="study_pubmed_id" value="Test study pubmedID"/> 637 <param name="study_pubmed_id" value="Test study pubmedID"/>
631 <repeat name="rep_sample"> 638 <repeat name="rep_sample">
632 <param name="sample_title" value="Test Sample title"/> 639 <param name="sample_title" value="Test Sample title"/>
633 <param name="sample_description" value="Test Sample description"/> 640 <param name="sample_description" value="Test Sample description"/>
634 <param name="scientific_name" value="Test Sample scientific name"/> 641 <param name="scientific_name" value="Test Sample scientific name"/>
635 <param name="tax_id" value="Test Sample tax_id"/> 642 <param name="tax_id" value="2697049"/>
636 <repeat name="rep_experiment"> 643 <repeat name="rep_experiment">
637 <param name="experiment_title" value="Test experiment title"/> 644 <param name="experiment_title" value="Test experiment title"/>
638 <param name="experiment_design" value="Test experiment design description"/> 645 <param name="experiment_design" value="Test experiment design description"/>
639 <param name="library_strategy" value="CTS"/> 646 <param name="library_strategy" value="CTS"/>
640 <param name="library_source" value="GENOMIC"/> 647 <param name="library_source" value="GENOMIC"/>
658 <has_text_matching expression="No ENA credentials defined"/> 665 <has_text_matching expression="No ENA credentials defined"/>
659 </assert_stdout> 666 </assert_stdout>
660 </test> 667 </test>
661 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples 668 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
662 also tests compression of uncompressed inputs and adding the .gz suffix --> 669 also tests compression of uncompressed inputs and adding the .gz suffix -->
663 <test expect_failure="true"> 670 <test expect_failure="false">
664 <conditional name="action_options"> 671 <conditional name="action_options">
665 <param name="action" value="add"/> 672 <param name="action" value="add"/>
666 <section name="test_submit_parameters"> 673 <section name="test_submit_parameters">
667 <param name="submit_dev" value="true" /> 674 <param name="submit_dev" value="true" />
668 <param name="dry_run" value="false" /> 675 <param name="dry_run" value="true" />
669 </section> 676 </section>
670 <param name="test_submit" value="True"/> 677 <param name="test_submit" value="True"/>
671 <conditional name="input_format_conditional"> 678 <conditional name="input_format_conditional">
672 <param name="add_extension" value="true"/> 679 <param name="add_extension" value="false"/>
673 <param name="input_format" value="build_tables"/> 680 <param name="input_format" value="build_tables"/>
674 <conditional name="conditional_viral_metadata"> 681 <conditional name="conditional_viral_metadata">
675 <param name="viral_sample" value="false"/> 682 <param name="viral_sample" value="false"/>
676 <repeat name="rep_study"> 683 <repeat name="rep_study">
677 <param name="study_title" value="Test study title"/> 684 <param name="study_title" value="Test study title"/>
680 <param name="study_pubmed_id" value="Test study pubmedID"/> 687 <param name="study_pubmed_id" value="Test study pubmedID"/>
681 <repeat name="rep_sample"> 688 <repeat name="rep_sample">
682 <param name="sample_title" value="Test Sample title"/> 689 <param name="sample_title" value="Test Sample title"/>
683 <param name="sample_description" value="Test Sample description"/> 690 <param name="sample_description" value="Test Sample description"/>
684 <param name="scientific_name" value="Test Sample scientific name"/> 691 <param name="scientific_name" value="Test Sample scientific name"/>
685 <param name="tax_id" value="Test Sample tax_id"/> 692 <param name="tax_id" value="2697049"/>
686 <repeat name="rep_experiment"> 693 <repeat name="rep_experiment">
687 <param name="experiment_title" value="Test experiment title"/> 694 <param name="experiment_title" value="Test experiment title"/>
688 <param name="experiment_design" value="Test experiment design description"/> 695 <param name="experiment_design" value="Test experiment design description"/>
689 <param name="library_strategy" value="CTS"/> 696 <param name="library_strategy" value="CTS"/>
690 <param name="library_source" value="GENOMIC"/> 697 <param name="library_source" value="GENOMIC"/>
694 <param name="library_construction_protocol" value="Test library construction"/> 701 <param name="library_construction_protocol" value="Test library construction"/>
695 <param name="platform" value="ILLUMINA"/> 702 <param name="platform" value="ILLUMINA"/>
696 <param name="instrument_model" value="Illumina HiSeq 4000"/> 703 <param name="instrument_model" value="Illumina HiSeq 4000"/>
697 <repeat name="rep_runs"> 704 <repeat name="rep_runs">
698 <param name="run_base_name" value="run_from_hospital_X"/> 705 <param name="run_base_name" value="run_from_hospital_X"/>
699 <param name="upload_files" value="sample.fq,sample.fq" ftype="fastqsanger"/> 706 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
700 </repeat> 707 </repeat>
701 </repeat> 708 </repeat>
702 </repeat> 709 </repeat>
703 </repeat> 710 </repeat>
704 </conditional> 711 </conditional>
705 </conditional> 712 </conditional>
706 </conditional> 713 </conditional>
707 <param name="center" value="Some research center"/> 714 <param name="center" value="Some research center"/>
708 <assert_command> 715 <assert_command>
709 <has_text_matching expression="ena-upload-cli"/> 716 <has_text_matching expression="ena-upload-cli"/>
710 <has_text_matching expression="--data 'sample.fq.fastq.gz' 'sample.fq.fastq.gz'"/> 717 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
711 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 718 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
712 <not_has_text text="modify" /> 719 <not_has_text text="modify" />
713 </assert_command> 720 </assert_command>
714 <assert_stderr>
715 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
716 </assert_stderr>
717 </test> 721 </test>
718 <!--Test 8: viral submission - User input metadata - Add extension = False--> 722 <!--Test 8: viral submission - User input metadata - Add extension = False-->
719 <test expect_failure="true"> 723 <test expect_failure="false">
720 <conditional name="action_options"> 724 <conditional name="action_options">
721 <param name="action" value="add"/> 725 <param name="action" value="add"/>
722 <section name="test_submit_parameters"> 726 <section name="test_submit_parameters">
723 <param name="submit_dev" value="false" /> 727 <param name="submit_dev" value="false" />
724 <param name="dry_run" value="false" /> 728 <param name="dry_run" value="true" />
725 </section> 729 </section>
726 <param name="test_submit" value="True"/> 730 <param name="test_submit" value="True"/>
727 <conditional name="input_format_conditional"> 731 <conditional name="input_format_conditional">
728 <param name="add_extension" value="False"/> 732 <param name="add_extension" value="false"/>
729 <param name="input_format" value="build_tables"/> 733 <param name="input_format" value="build_tables"/>
730 <conditional name="conditional_viral_metadata"> 734 <conditional name="conditional_viral_metadata">
731 <param name="viral_sample" value="true"/> 735 <param name="viral_sample" value="true"/>
732 <repeat name="rep_study"> 736 <repeat name="rep_study">
733 <param name="study_title" value="Test study title"/> 737 <param name="study_title" value="Test study title"/>
736 <param name="study_pubmed_id" value="Test study pubmedID"/> 740 <param name="study_pubmed_id" value="Test study pubmedID"/>
737 <repeat name="rep_sample"> 741 <repeat name="rep_sample">
738 <param name="sample_title" value="Test Sample title"/> 742 <param name="sample_title" value="Test Sample title"/>
739 <param name="sample_description" value="Test Sample description"/> 743 <param name="sample_description" value="Test Sample description"/>
740 <param name="scientific_name" value="Test Sample scientific name"/> 744 <param name="scientific_name" value="Test Sample scientific name"/>
741 <param name="tax_id" value="Test Sample tax_id"/> 745 <param name="tax_id" value="2697049"/>
742 <param name="collection_date" value="2020"/> 746 <param name="collection_date" value="2020"/>
743 <param name="geo_location_country" value="Belgium"/> 747 <param name="geo_location_country" value="Belgium"/>
744 <param name="host_common_name" value="Human"/> 748 <param name="host_common_name" value="Human"/>
745 <param name="host_subject_id" value="Patient_001"/> 749 <param name="host_subject_id" value="Patient_001"/>
746 <param name="host_health_state" value="healthy"/> 750 <param name="host_health_state" value="healthy"/>
775 <has_text_matching expression="ena-upload-cli"/> 779 <has_text_matching expression="ena-upload-cli"/>
776 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> 780 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
777 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 781 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
778 <has_text_matching expression="--checklist ERC000033"/> 782 <has_text_matching expression="--checklist ERC000033"/>
779 </assert_command> 783 </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>
784 <!--Test 9: modify option and auto compression - viral submission - User input metadata--> 785 <!--Test 9: modify option and auto compression - viral submission - User input metadata-->
785 <test expect_failure="true"> 786 <test expect_failure="false">
786 <conditional name="action_options"> 787 <conditional name="action_options">
787 <param name="action" value="modify"/> 788 <param name="action" value="modify"/>
788 <section name="test_submit_parameters"> 789 <section name="test_submit_parameters">
789 <param name="submit_dev" value="false" /> 790 <param name="submit_dev" value="false" />
790 <param name="dry_run" value="false" /> 791 <param name="dry_run" value="true" />
791 </section> 792 </section>
792 <param name="test_submit" value="True"/> 793 <param name="test_submit" value="True"/>
793 <conditional name="input_format_conditional"> 794 <conditional name="input_format_conditional">
794 <param name="add_extension" value="False"/> 795 <param name="add_extension" value="fasle"/>
795 <param name="input_format" value="build_tables"/> 796 <param name="input_format" value="build_tables"/>
796 <conditional name="conditional_viral_metadata"> 797 <conditional name="conditional_viral_metadata">
797 <param name="viral_sample" value="True"/> 798 <param name="viral_sample" value="True"/>
798 <repeat name="rep_study"> 799 <repeat name="rep_study">
799 <param name="study_title" value="Test study title"/> 800 <param name="study_title" value="Test study title"/>
802 <param name="study_pubmed_id" value="Test study pubmedID"/> 803 <param name="study_pubmed_id" value="Test study pubmedID"/>
803 <repeat name="rep_sample"> 804 <repeat name="rep_sample">
804 <param name="sample_title" value="Test Sample title"/> 805 <param name="sample_title" value="Test Sample title"/>
805 <param name="sample_description" value="Test Sample description"/> 806 <param name="sample_description" value="Test Sample description"/>
806 <param name="scientific_name" value="Test Sample scientific name"/> 807 <param name="scientific_name" value="Test Sample scientific name"/>
807 <param name="tax_id" value="Test Sample tax_id"/> 808 <param name="tax_id" value="2697049"/>
808 <param name="collection_date" value="2020"/> 809 <param name="collection_date" value="2020"/>
809 <param name="geo_location_country" value="Belgium"/> 810 <param name="geo_location_country" value="Belgium"/>
810 <param name="host_common_name" value="Human"/> 811 <param name="host_common_name" value="Human"/>
811 <param name="host_subject_id" value="Patient_001"/> 812 <param name="host_subject_id" value="Patient_001"/>
812 <param name="host_health_state" value="healthy"/> 813 <param name="host_health_state" value="healthy"/>
826 <param name="library_construction_protocol" value="Test library construction"/> 827 <param name="library_construction_protocol" value="Test library construction"/>
827 <param name="platform" value="ILLUMINA"/> 828 <param name="platform" value="ILLUMINA"/>
828 <param name="instrument_model" value="Illumina HiSeq 4000"/> 829 <param name="instrument_model" value="Illumina HiSeq 4000"/>
829 <repeat name="rep_runs"> 830 <repeat name="rep_runs">
830 <param name="run_base_name" value="run_from_hospital_X"/> 831 <param name="run_base_name" value="run_from_hospital_X"/>
831 <param name="upload_files" value="sample.fq" ftype="fastqsanger"/> 832 <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/>
832 </repeat> 833 </repeat>
833 </repeat> 834 </repeat>
834 </repeat> 835 </repeat>
835 </repeat> 836 </repeat>
836 </conditional> 837 </conditional>
837 </conditional> 838 </conditional>
838 </conditional> 839 </conditional>
839 <param name="center" value="Some research center"/> 840 <param name="center" value="Some research center"/>
840 <assert_command> 841 <assert_command>
841 <has_text_matching expression="ena-upload-cli"/> 842 <has_text_matching expression="ena-upload-cli"/>
842 <has_text_matching expression="--data 'sample.fq.gz'"/> 843 <has_text_matching expression="--data '1.fastqsanger.gz'"/>
843 <has_text_matching expression="--action 'modify' --center 'Some research center'"/> 844 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
844 <has_text_matching expression="--checklist ERC000033"/> 845 <has_text_matching expression="--checklist ERC000033"/>
845 <not_has_text text="add" /> 846 <not_has_text text="add" />
846 </assert_command> 847 </assert_command>
847 <assert_stderr>
848 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
849 </assert_stderr>
850 </test> 848 </test>
851 </tests> 849 </tests>
852 <help><![CDATA[ 850 <help><![CDATA[
853 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli 851 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
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 852 The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
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 853 It is also possible to submit an excel file by following the template in https://github.com/ELIXIR-Belgium/ENA-metadata-templates
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> 854 ]]></help>
858 <citations> 855 <citations>
859 </citations> 856 </citations>
860 </tool> 857 </tool>