Mercurial > repos > ieguinoa > ena_upload
comparison ena_upload.xml @ 2:2f7a70c0d3ab draft default tip
Uploaded
| author | ieguinoa |
|---|---|
| date | Mon, 21 Feb 2022 14:22:53 +0000 |
| parents | 5d59238cd3f4 |
| children |
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| 1:9681a9180730 | 2:2f7a70c0d3ab |
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| 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> |