ena_upload: ena_upload.xml annotate

annotate ena_upload.xml @ 3:59bb6d34fca6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 28d2a0cfcbb04d88b6e19a7d898a2bada3bce149"

author	iuc
date	Wed, 18 Aug 2021 19:42:49 +0000
parents	9e2df763086c
children	26ccb678abc8

rev	line source
3 59bb6d34fca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 28d2a0cfcbb04d88b6e19a7d898a2bada3bce149" iuc parents: 2 diff changeset	1 <tool id="ena_upload" name="ENA Upload tool" version="0.3.3" profile="20.01" license="MIT">
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	2 <macros>
2 9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	3 <token name="@VERSION@">0.3.1</token>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	4 <import>samples_macros.xml</import>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	5 </macros>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	6 <requirements>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	8 <requirement type="package" version="1.2.0">xlrd</requirement>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	9 </requirements>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	10 <stdio>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	11 <regex match="Oops" source="stderr" level="fatal"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	12 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	13 </stdio>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	14 <command detect_errors="exit_code"><![CDATA[
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	15 mkdir ./submission_files;
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	16 #set $studies_table_path = './submission_files/studies.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	17 #set $samples_table_path = './submission_files/samples.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	18 #set $experiments_table_path = './submission_files/experiments.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	19 #set $runs_table_path = './submission_files/runs.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	20
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	21 #set $studies_table_path_updated = './submission_files/studies_updated.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	22 #set $samples_table_path_updated = './submission_files/samples_updated.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	23 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	24 #set $runs_table_path_updated = './submission_files/runs_updated.tsv'
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	25
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	26 #set working_dir = os.getcwd()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	27 #if $action_options.input_format_conditional.input_format == "build_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	28 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	29 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	30
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	31 #if $action_options.input_format_conditional.input_format == "excel_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	32 python '$__tool_directory__/process_xlsx.py'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	33 #if $action_options.input_format_conditional.viral_submission == "true":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	34 --vir
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	35 #end if
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	36 --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files --verbose > '$output';
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	37 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	38
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	39 #if $action_options.input_format_conditional.input_format != "user_generated_tables":
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	40 cp $studies_table_path $studies_table_out &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	41 cp $samples_table_path $samples_table_out &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	42 cp $experiments_table_path $experiments_table_out &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	43 cp $runs_table_path $runs_table_out &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	44 #else:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	45 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	46 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	47 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	48 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	49 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	50
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	51 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	52 webin_id=`grep 'username' $credentials`;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	53 if [ "\$webin_id" = "" ]; then
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	54 ## No credentials in user defined preferences
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	55 ## Fallback to global defined credentials (if exist)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	56 #import os
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	57 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	58 credentials_path=\${GALAXY_ENA_SECRETS};
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	59 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	60 if [ "\$webin_id" = "" ]; then
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	61 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	62 exit 1;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	63 fi;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	64 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	65 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	66 exit 1;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	67 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	68 else
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	69 credentials_path='$credentials';
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	70 fi;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	71 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	72
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	73 #if $action_options.test_submit == "True":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	74 credentials_path='test_fake_path';
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	75 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	76
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	77 ## create the list of files to upload and make the symlinks
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	78 #import re
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	79 #set $files_to_upload = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	80 #if $action_options.input_format_conditional.input_format == "build_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	81 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	82 #for $sample in $study.rep_sample:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	83 #for $experiment in $sample.rep_experiment:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	84 #for $run in $experiment.rep_runs:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	85 #for $file in $run.upload_files:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	86 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	87 ln -s '$file' $safename_reads_file &&
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	88 $files_to_upload.append(str($safename_reads_file))
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	89 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	90 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	91 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	92 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	93 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	94 #else:
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	95 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list':
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	96 #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	97 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	98 #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	99 #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq.gz'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	100 #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	101 #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq.bz2'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	102 #else:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	103 #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	104 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	105 #if $pair.reverse.is_of_type('fastq.gz', 'fastqsanger.gz'):
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	106 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq.gz'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	107 #elif $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	108 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq.bz2'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	109 #else:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	110 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	111 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	112
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	113 ln -s '$pair.forward' $safename_fwd_reads_file &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	114 $files_to_upload.append(str($safename_fwd_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	115 ln -s '$pair.reverse' $safename_rev_reads_file &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	116 $files_to_upload.append(str($safename_rev_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	117 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	118 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	119 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	120 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	121 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	122 ln -s '$file' $safename_reads_file &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	123 $files_to_upload.append(str($safename_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	124 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	125 #end if
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	126 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	127
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	128
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	129 #if $action_options.test_submit_parameters.dry_run == "false":
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	130 ena-upload-cli
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	131 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	132 --action '$action_options.action'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	133 --center '$action_options.center'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	134 --secret \${credentials_path}
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	135 --data
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	136 #for $dataset in $files_to_upload:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	137 '$dataset'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	138 #end for
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	139 --experiment '$experiments_table_path'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	140 --study '$studies_table_path'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	141 --run '$runs_table_path'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	142 --sample '$samples_table_path'
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	143 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	144 #if "$action_options.input_format_conditional.viral_submission" == "true":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	145 --vir
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	146 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	147 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	148 #if $action_options.input_format_conditional.input_format == "build_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	149 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	150 --vir
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	151 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	152 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	153 #if $action_options.input_format_conditional.viral_submission == "true":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	154 --vir
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	155 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	156 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	157 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	158
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	159 #if $action_options.test_submit_parameters.submit_dev == "true":
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	160 -d
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	161 #end if
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	162 >> '$output';
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	163 echo -e 'center_name\t$action_options.center' >> '$output';
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	164 echo -e 'action_option\t$action_options.action' >> '$output';
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	165 #if $action_options.input_format_conditional.input_format != "user_generated_tables":
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	166 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	167 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	168 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	169 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	170 #end if
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	171 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	172 exit 0;
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	173 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	174
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	175 ]]></command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	176 <configfiles>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	177 <configfile name="credentials"><![CDATA[
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	178 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account\|webin_id', "").strip()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	179 #set $password = $__user__.extra_preferences.get('ena_webin_account\|password', "").strip()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	180 #if $webin_id != "":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	181 username: "$webin_id"
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	182 password: "$password"
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	183 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	184 ]]></configfile>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	185 <configfile name="studies_json">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	186 #import json
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	187 #import re
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	188 #if $action_options.input_format_conditional.input_format == "build_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	189 #set $files_to_upload = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	190 #set $studies = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	191 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	192 #set samples = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	193 #for $sample in $study.rep_sample:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	194 #set experiments = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	195 #for $experiment in $sample.rep_experiment:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	196 #set runs = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	197 #for $run in $experiment.rep_runs:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	198 #set run_files = list()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	199 #for $file in $run.upload_files:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	200 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	201 $run_files.append(str($safename_reads_file))
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	202 #end for
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	203 $runs.append((str($run.run_base_name),$run_files))
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	204 #end for
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	205
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	206 $experiments.append({'title':str($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})
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	207 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	208 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	209
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	210 $samples.append({'title':str($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})
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	211 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	212
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	213 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'experiments':$experiments})
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	214 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	215 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	216 $studies.append({'title':str($study.study_title),'type':str($study.study_type),'abstract':str($study.study_abstract),'pubmed_id':str($study.study_pubmed_id),'samples':$samples})
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	217 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	218 #echo $json.dumps($studies)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	219 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	220 </configfile>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	221 </configfiles>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	222 <inputs>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	223 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	224 <param name="action" type="select" label="Action to execute">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	225 <option value="add" selected="True">Add new data</option>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	226 <option value="modify">Modify metadata</option>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	227 </param>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	228 <when value="add">
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	229 <expand macro="test_submit_section"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	230 <param name="test_submit" type="hidden" value="False" />
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	231 <expand macro="table_inputs_macro" />
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	232 </when>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	233 <when value="modify">
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	234 <expand macro="test_submit_section"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	235 <expand macro="table_inputs_macro" />
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	236 </when>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	237 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	238 </inputs>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	239 <outputs>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	240 <data name="output" format="txt" label="ENA submission receipt"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	241 <data name="studies_table_out" format="tabular" label="Studies table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	242 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	243 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	244 <data name="samples_table_out" format="tabular" label="Samples table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	245 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	246 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	247 <data name="experiments_table_out" format="tabular" label="Experiments table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	248 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	249 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	250 <data name="runs_table_out" format="tabular" label="Runs table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	251 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	252 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	253 </outputs>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	254 <tests>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	255 <!--Test excel input of VIRAL samples -->
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	256 <test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	257 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	258 <param name="action" value="add"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	259 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	260 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	261 <param name="dry_run" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	262 </section>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	263 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	264 <param name="input_format" value="excel_tables"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	265 <param name="viral_submission" value="True"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	266 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	267 <conditional name="run_input_format_conditional">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	268 <param name="run_input_format" value="multiple_selection_list"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	269 <param name="data" value="sample.fq"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	270 </conditional>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	271 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	272 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	273 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	274 <output name="experiments_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	275 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	276 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	277 <has_n_columns n="17"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	278 <has_line_matching expression="alias\tstatus\taccession\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\tsubmission_date" />
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	279 <has_line_matching expression="e_(.)_026\tadd\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.)"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	280 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	281 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	282 <output name="studies_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	283 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	284 <has_n_lines n="2"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	285 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	286 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	287 <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\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(.*)"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	288 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	289 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	290 <output name="samples_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	291 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	292 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	293 <has_n_columns n="18"/>
2 9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	294 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	295 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	296 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	297 <output name="runs_table_out">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	298 <assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	299 <has_n_lines n="5"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	300 <has_n_columns n="8"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	301 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	302 <has_line_matching expression="r_(.)_026\tadd\tena_run_accession\te_(.)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	303 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	304 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	305 </test>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	306 <!--Test excel input of VIRAL samples with extended columns-->
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	307 <test>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	308 <conditional name="action_options">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	309 <param name="action" value="add"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	310 <section name="test_submit_parameters">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	311 <param name="submit_dev" value="false" />
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	312 <param name="dry_run" value="true" />
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	313 </section>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	314 <conditional name="input_format_conditional">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	315 <param name="input_format" value="excel_tables"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	316 <param name="viral_submission" value="True"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	317 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	318 <conditional name="run_input_format_conditional">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	319 <param name="run_input_format" value="multiple_selection_list"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	320 <param name="data" value="sample.fq"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	321 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	322 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	323 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	324 <param name="center" value="Some research center"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	325 <output name="experiments_table_out">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	326 <assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	327 <has_n_lines n="5"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	328 <has_n_columns n="17"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	329 <has_line_matching expression="alias\tstatus\taccession\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\tsubmission_date" />
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	330 <has_line_matching expression="e_(.)_026\tadd\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.)"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	331 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	332 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	333 <output name="studies_table_out">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	334 <assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	335 <has_n_lines n="2"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	336 <has_n_columns n="8"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	337 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	338 <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\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(.*)"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	339 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	340 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	341 <output name="samples_table_out">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	342 <assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	343 <has_n_lines n="5"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	344 <has_n_columns n="42"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	345 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date\tgeographic_location_latitude\tgeographic_location_longitude\tsample_capture_status\thost_disease_outcome\thost_age\tvirus_identifier\treceipt_date\tdefinition_for_seropositive_sample\tserotype\thost_habitat\tisolation_source_host_associated\thost_behaviour\tisolation_source_non_host_associated\tsubject_exposure\tsubject_exposure_duration\ttype_exposure\tpersonal_protective_equipment\thospitalisation\tillness_duration\tillness_symptoms\tsample_storage_conditions\tstrain\thost_description\tgravidity"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	346 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	347 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	348 <output name="runs_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	349 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	350 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	351 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	352 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	353 <has_line_matching expression="r_(.)_026\tadd\tena_run_accession\te_(.)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	354 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	355 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	356 </test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	357 <!--Test excel input of NON-VIRAL samples-->
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	358 <test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	359 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	360 <param name="action" value="add"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	361 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	362 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	363 <param name="dry_run" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	364 </section>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	365 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	366 <param name="input_format" value="excel_tables"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	367 <param name="viral_submission" value="False"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	368 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	369 <conditional name="run_input_format_conditional">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	370 <param name="run_input_format" value="multiple_selection_list"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	371 <param name="data" value="sample.fq"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	372 </conditional>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	373 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	374 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	375 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	376 <output name="experiments_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	377 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	378 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	379 <has_n_columns n="17"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	380 <has_line_matching expression="alias\tstatus\taccession\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\tsubmission_date" />
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	381 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	382 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	383 <output name="studies_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	384 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	385 <has_n_lines n="2"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	386 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	387 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	388 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	389 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	390 <output name="samples_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	391 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	392 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	393 <has_n_columns n="8"/>
2 9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	394 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	395 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	396 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	397 <output name="runs_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	398 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	399 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	400 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	401 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	402 <has_line_matching expression="r_(.)_026\tadd\tena_run_accession\te_(.)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	403 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	404 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	405 </test>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	406 <!--Test failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	407 <test expect_failure="true">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	408 <conditional name="action_options">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	409 <param name="action" value="add"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	410 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	411 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	412 <param name="dry_run" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	413 </section>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	414 <conditional name="input_format_conditional">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	415 <param name="input_format" value="excel_tables"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	416 <param name="viral_submission" value="False"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	417 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	418 <conditional name="run_input_format_conditional">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	419 <param name="run_input_format" value="paired_list"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	420 <param name="paired_end_collection">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	421 <collection type="list:paired">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	422 <element name="paired_run_name">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	423 <collection type="paired">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	424 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	425 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	426 </collection>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	427 </element>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	428 </collection>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	429 </param>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	430 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	431 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	432 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	433 <param name="center" value="Some research center"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	434 <assert_command>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	435 <has_text_matching expression="ena-upload-cli"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	436 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	437 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	438 </assert_command>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	439 </test>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	440 <!--Test build tables from user input fields NON-VIRAL samples-->
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	441 <test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	442 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	443 <param name="action" value="add"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	444 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	445 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	446 <param name="dry_run" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	447 </section>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	448 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	449 <param name="input_format" value="build_tables"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	450 <conditional name="conditional_viral_metadata">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	451 <param name="viral_sample" value="False"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	452 <repeat name="rep_study">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	453 <param name="study_title" value="Test study title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	454 <param name="study_abstract" value="Test study abstract"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	455 <param name="study_type" value="Epigenetics"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	456 <param name="study_pubmed_id" value="Test study pubmedID"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	457 <repeat name="rep_sample">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	458 <param name="sample_title" value="Test Sample title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	459 <param name="sample_description" value="Test Sample description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	460 <param name="scientific_name" value="Test Sample scientific name"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	461 <param name="tax_id" value="Test Sample tax_id"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	462 <repeat name="rep_experiment">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	463 <param name="experiment_title" value="Test experiment title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	464 <param name="experiment_design" value="Test experiment design description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	465 <param name="library_strategy" value="CTS"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	466 <param name="library_source" value="GENOMIC"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	467 <param name="library_selection" value="PCR"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	468 <param name="library_layout" value="SINGLE"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	469 <param name="insert_size" value="150"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	470 <param name="library_construction_protocol" value="Test library construction"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	471 <param name="platform" value="ILLUMINA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	472 <param name="instrument_model" value="Illumina HiSeq 4000"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	473 <repeat name="rep_runs">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	474 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	475 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	476 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	477 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	478 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	479 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	480 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	481 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	482 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	483 <output name="experiments_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	484 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	485 <has_n_lines n="2"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	486 <has_n_columns n="17"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	487 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	488 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	489 <output name="studies_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	490 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	491 <has_n_lines n="2"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	492 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	493 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	494 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	495 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	496 <output name="samples_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	497 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	498 <has_n_lines n="2"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	499 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	500 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	501 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	502 <output name="runs_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	503 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	504 <has_n_lines n="3"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	505 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	506 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	507 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	508 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	509 </test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	510 <!--Test RUN failing build tables from user input fields NON-VIRAL samples-->
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	511 <test expect_failure="true">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	512 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	513 <param name="action" value="add"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	514 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	515 <param name="submit_dev" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	516 <param name="dry_run" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	517 </section>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	518 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	519 <param name="input_format" value="build_tables"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	520 <conditional name="conditional_viral_metadata">
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	521 <param name="viral_sample" value="false"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	522 <repeat name="rep_study">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	523 <param name="study_title" value="Test study title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	524 <param name="study_abstract" value="Test study abstract"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	525 <param name="study_type" value="Epigenetics"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	526 <param name="study_pubmed_id" value="Test study pubmedID"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	527 <repeat name="rep_sample">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	528 <param name="sample_title" value="Test Sample title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	529 <param name="sample_description" value="Test Sample description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	530 <param name="scientific_name" value="Test Sample scientific name"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	531 <param name="tax_id" value="Test Sample tax_id"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	532 <repeat name="rep_experiment">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	533 <param name="experiment_title" value="Test experiment title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	534 <param name="experiment_design" value="Test experiment design description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	535 <param name="library_strategy" value="CTS"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	536 <param name="library_source" value="GENOMIC"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	537 <param name="library_selection" value="PCR"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	538 <param name="library_layout" value="SINGLE"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	539 <param name="insert_size" value="150"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	540 <param name="library_construction_protocol" value="Test library construction"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	541 <param name="platform" value="ILLUMINA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	542 <param name="instrument_model" value="Illumina HiSeq 4000"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	543 <repeat name="rep_runs">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	544 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	545 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	546 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	547 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	548 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	549 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	550 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	551 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	552 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	553 <assert_stdout>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	554 <has_text_matching expression="No ENA credentials defined"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	555 </assert_stdout>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	556 </test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	557 <!--Test with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples-->
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	558 <test expect_failure="true">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	559 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	560 <param name="action" value="add"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	561 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	562 <param name="submit_dev" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	563 <param name="dry_run" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	564 </section>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	565 <param name="test_submit" value="True"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	566 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	567 <param name="input_format" value="build_tables"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	568 <conditional name="conditional_viral_metadata">
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	569 <param name="viral_sample" value="false"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	570 <repeat name="rep_study">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	571 <param name="study_title" value="Test study title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	572 <param name="study_abstract" value="Test study abstract"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	573 <param name="study_type" value="Epigenetics"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	574 <param name="study_pubmed_id" value="Test study pubmedID"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	575 <repeat name="rep_sample">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	576 <param name="sample_title" value="Test Sample title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	577 <param name="sample_description" value="Test Sample description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	578 <param name="scientific_name" value="Test Sample scientific name"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	579 <param name="tax_id" value="Test Sample tax_id"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	580 <repeat name="rep_experiment">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	581 <param name="experiment_title" value="Test experiment title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	582 <param name="experiment_design" value="Test experiment design description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	583 <param name="library_strategy" value="CTS"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	584 <param name="library_source" value="GENOMIC"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	585 <param name="library_selection" value="PCR"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	586 <param name="library_layout" value="SINGLE"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	587 <param name="insert_size" value="150"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	588 <param name="library_construction_protocol" value="Test library construction"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	589 <param name="platform" value="ILLUMINA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	590 <param name="instrument_model" value="Illumina HiSeq 4000"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	591 <repeat name="rep_runs">
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	592 <param name="run_base_name" value="run_from_hospital_X"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	593 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	594 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	595 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	596 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	597 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	598 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	599 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	600 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	601 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	602 <assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	603 <has_text_matching expression="ena-upload-cli"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	604 <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	605 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	606 </assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	607 <assert_stderr>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	608 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	609 </assert_stderr>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	610 </test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	611 <!--test viral submission - User input metadata-->
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	612 <test expect_failure="true">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	613 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	614 <param name="action" value="add"/>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	615 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	616 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	617 <param name="dry_run" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	618 </section>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	619 <param name="test_submit" value="True"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	620 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	621 <param name="input_format" value="build_tables"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	622 <conditional name="conditional_viral_metadata">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	623 <param name="viral_sample" value="True"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	624 <repeat name="rep_study">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	625 <param name="study_title" value="Test study title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	626 <param name="study_abstract" value="Test study abstract"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	627 <param name="study_type" value="Epigenetics"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	628 <param name="study_pubmed_id" value="Test study pubmedID"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	629 <repeat name="rep_sample">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	630 <param name="sample_title" value="Test Sample title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	631 <param name="sample_description" value="Test Sample description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	632 <param name="scientific_name" value="Test Sample scientific name"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	633 <param name="tax_id" value="Test Sample tax_id"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	634 <param name="collection_date" value="2020"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	635 <param name="geo_location_country" value="Belgium"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	636 <param name="host_common_name" value="Human"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	637 <param name="host_subject_id" value="Patient_001"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	638 <param name="host_health_state" value="healthy"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	639 <param name="host_sex" value="female"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	640 <param name="host_scientific_name" value="homo sapiens"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	641 <param name="collector_name" value="John The Collector"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	642 <param name="collecting_institution" value="Hospital 01"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	643 <param name="isolate" value="sample_001"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	644 <repeat name="rep_experiment">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	645 <param name="experiment_title" value="Test experiment title"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	646 <param name="experiment_design" value="Test experiment design description"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	647 <param name="library_strategy" value="CTS"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	648 <param name="library_source" value="GENOMIC"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	649 <param name="library_selection" value="PCR"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	650 <param name="library_layout" value="SINGLE"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	651 <param name="insert_size" value="150"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	652 <param name="library_construction_protocol" value="Test library construction"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	653 <param name="platform" value="ILLUMINA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	654 <param name="instrument_model" value="Illumina HiSeq 4000"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	655 <repeat name="rep_runs">
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	656 <param name="run_base_name" value="run_from_hospital_X"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	657 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	658 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	659 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	660 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	661 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	662 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	663 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	664 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	665 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	666 <assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	667 <has_text_matching expression="ena-upload-cli"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	668 <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	669 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	670 <has_text_matching expression="--vir"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	671 </assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	672 <assert_stderr>
1 57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd" iuc parents: 0 diff changeset	673 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	674 </assert_stderr>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	675 </test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	676 </tests>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	677 <help><![CDATA[
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	678 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	679 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
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	680 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
2 9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e" iuc parents: 1 diff changeset	681 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
0 382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	682 ]]></help>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	683 <citations>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	684 </citations>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" iuc parents: diff changeset	685 </tool>

Mercurial > repos > iuc > ena_upload

annotate ena_upload.xml @ 3:59bb6d34fca6 draft