annotate ena_upload.xml @ 2:9e2df763086c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
author iuc
date Thu, 15 Jul 2021 20:12:34 +0000
parents 57251c760cab
children 59bb6d34fca6
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1 <tool id="ena_upload" name="ENA Upload tool" version="0.3.2" profile="20.01" license="MIT">
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2 <macros>
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3 <token name="@VERSION@">0.3.1</token>
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4 <import>samples_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
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8 <requirement type="package" version="1.2.0">xlrd</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="Oops" source="stderr" level="fatal"/>
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12 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 mkdir ./submission_files;
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16 #set $studies_table_path = './submission_files/studies.tsv'
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17 #set $samples_table_path = './submission_files/samples.tsv'
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18 #set $experiments_table_path = './submission_files/experiments.tsv'
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19 #set $runs_table_path = './submission_files/runs.tsv'
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21 #set $studies_table_path_updated = './submission_files/studies_updated.tsv'
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22 #set $samples_table_path_updated = './submission_files/samples_updated.tsv'
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23 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv'
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24 #set $runs_table_path_updated = './submission_files/runs_updated.tsv'
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25
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26 #set working_dir = os.getcwd()
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27 #if $action_options.input_format_conditional.input_format == "build_tables":
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28 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
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29 #end if
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30
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31 #if $action_options.input_format_conditional.input_format == "excel_tables":
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32 python '$__tool_directory__/process_xlsx.py'
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33 #if $action_options.input_format_conditional.viral_submission == "true":
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34 --vir
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35 #end if
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36 --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files --verbose > '$output';
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37 #end if
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38
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39 #if $action_options.input_format_conditional.input_format != "user_generated_tables":
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40 cp $studies_table_path $studies_table_out &&
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41 cp $samples_table_path $samples_table_out &&
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42 cp $experiments_table_path $experiments_table_out &&
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43 cp $runs_table_path $runs_table_out &&
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44 #else:
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45 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
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46 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
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47 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
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48 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
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49 #end if
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50
1
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51 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
0
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52 webin_id=`grep 'username' $credentials`;
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53 if [ "\$webin_id" = "" ]; then
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54 ## No credentials in user defined preferences
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55 ## Fallback to global defined credentials (if exist)
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56 #import os
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57 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
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58 credentials_path=\${GALAXY_ENA_SECRETS};
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59 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
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60 if [ "\$webin_id" = "" ]; then
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61 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
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62 exit 1;
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63 fi;
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64 #else:
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65 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
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66 exit 1;
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67 #end if
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68 else
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69 credentials_path='$credentials';
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70 fi;
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71 #end if
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72
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73 #if $action_options.test_submit == "True":
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74 credentials_path='test_fake_path';
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75 #end if
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76
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77 ## create the list of files to upload and make the symlinks
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78 #import re
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79 #set $files_to_upload = list()
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80 #if $action_options.input_format_conditional.input_format == "build_tables":
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81 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
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82 #for $sample in $study.rep_sample:
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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
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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
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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
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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
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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
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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
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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
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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
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102 #else:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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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
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diff changeset
109 #else:
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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110 #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
111 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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112
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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113 ln -s '$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
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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
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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
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117 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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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
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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
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121 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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122 ln -s '$file' $safename_reads_file &&
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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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
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124 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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125 #end if
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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126 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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127
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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128
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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129 #if $action_options.test_submit_parameters.dry_run == "false":
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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130 ena-upload-cli
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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131 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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132 --action '$action_options.action'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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133 --center '$action_options.center'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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134 --secret \${credentials_path}
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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135 --data
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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136 #for $dataset in $files_to_upload:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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137 '$dataset'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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138 #end for
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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139 --experiment '$experiments_table_path'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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140 --study '$studies_table_path'
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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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"
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diff changeset
143 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
144 #if "$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"
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diff changeset
145 --vir
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
146 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
147 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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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
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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
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diff changeset
150 --vir
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
151 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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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 $action_options.test_submit_parameters.submit_dev == "true":
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
160 -d
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
161 #end if
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
162 >> '$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
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168 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
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169 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
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170 #end if
0
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171 #else:
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172 exit 0;
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173 #end if
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174
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175 ]]></command>
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176 <configfiles>
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177 <configfile name="credentials"><![CDATA[
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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"
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179 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
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180 #if $webin_id != "":
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181 username: "$webin_id"
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182 password: "$password"
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183 #end if
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184 ]]></configfile>
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185 <configfile name="studies_json">
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186 #import json
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187 #import re
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188 #if $action_options.input_format_conditional.input_format == "build_tables":
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189 #set $files_to_upload = list()
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190 #set $studies = list()
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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"
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192 #set samples = list()
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193 #for $sample in $study.rep_sample:
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194 #set experiments = list()
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195 #for $experiment in $sample.rep_experiment:
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196 #set runs = list()
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197 #for $run in $experiment.rep_runs:
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198 #set run_files = list()
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199 #for $file in $run.upload_files:
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200 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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201 $run_files.append(str($safename_reads_file))
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202 #end for
1
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203 $runs.append((str($run.run_base_name),$run_files))
0
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204 #end for
1
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205
0
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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"
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207 #end for
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208 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
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209
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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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"
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211 #else:
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212
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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})
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214 #end if
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215 #end for
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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"
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217 #end for
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218 #echo $json.dumps($studies)
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219 #end if
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220 </configfile>
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221 </configfiles>
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222 <inputs>
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223 <conditional name="action_options">
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224 <param name="action" type="select" label="Action to execute">
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225 <option value="add" selected="True">Add new data</option>
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226 <option value="modify">Modify metadata</option>
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227 </param>
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228 <when value="add">
1
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229 <expand macro="test_submit_section"/>
0
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230 <param name="test_submit" type="hidden" value="False" />
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231 <expand macro="table_inputs_macro" />
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232 </when>
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233 <when value="modify">
1
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234 <expand macro="test_submit_section"/>
0
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235 <expand macro="table_inputs_macro" />
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236 </when>
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237 </conditional>
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238 </inputs>
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239 <outputs>
1
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240 <data name="output" format="txt" label="ENA submission receipt"/>
0
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241 <data name="studies_table_out" format="tabular" label="Studies table">
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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"
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243 </data>
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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"
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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"
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246 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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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"
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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"
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249 </data>
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250 <data name="runs_table_out" format="tabular" label="Runs table">
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251 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
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252 </data>
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253 </outputs>
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254 <tests>
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255 <!--Test excel input of VIRAL samples -->
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256 <test>
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257 <conditional name="action_options">
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258 <param name="action" value="add"/>
1
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259 <section name="test_submit_parameters">
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260 <param name="submit_dev" value="false" />
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261 <param name="dry_run" value="true" />
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262 </section>
0
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263 <conditional name="input_format_conditional">
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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"
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265 <param name="viral_submission" value="True"/>
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266 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
1
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267 <conditional name="run_input_format_conditional">
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268 <param name="run_input_format" value="multiple_selection_list"/>
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269 <param name="data" value="sample.fq"/>
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270 </conditional>
0
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271 </conditional>
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272 </conditional>
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273 <param name="center" value="Some research center"/>
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274 <output name="experiments_table_out">
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275 <assert_contents>
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276 <has_n_lines n="5"/>
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277 <has_n_columns n="17"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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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"
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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"
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280 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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281 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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282 <output name="studies_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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283 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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284 <has_n_lines n="2"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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285 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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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"
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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"
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288 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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289 </output>
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290 <output name="samples_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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291 <assert_contents>
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292 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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293 <has_n_columns n="18"/>
2
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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"
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295 </assert_contents>
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296 </output>
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297 <output name="runs_table_out">
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298 <assert_contents>
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299 <has_n_lines n="5"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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300 <has_n_columns n="8"/>
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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"
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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"
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303 </assert_contents>
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304 </output>
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305 </test>
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306 <!--Test excel input of VIRAL samples with extended columns-->
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307 <test>
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308 <conditional name="action_options">
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309 <param name="action" value="add"/>
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310 <section name="test_submit_parameters">
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311 <param name="submit_dev" value="false" />
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312 <param name="dry_run" value="true" />
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313 </section>
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314 <conditional name="input_format_conditional">
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315 <param name="input_format" value="excel_tables"/>
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316 <param name="viral_submission" value="True"/>
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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"
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318 <conditional name="run_input_format_conditional">
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319 <param name="run_input_format" value="multiple_selection_list"/>
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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"
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321 </conditional>
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322 </conditional>
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323 </conditional>
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324 <param name="center" value="Some research center"/>
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325 <output name="experiments_table_out">
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326 <assert_contents>
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327 <has_n_lines n="5"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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328 <has_n_columns n="17"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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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"
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330 <has_line_matching expression="e_(.*)_026\tadd\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
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331 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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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
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674 </assert_stderr>
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675 </test>
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676 </tests>
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677 <help><![CDATA[
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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678 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
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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
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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
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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
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682 ]]></help>
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683 <citations>
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684 </citations>
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685 </tool>