Mercurial > repos > iuc > ena_upload

annotate ena_upload.xml @ 11:f803a68fc9e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
author iuc
date Sat, 23 Mar 2024 22:06:45 +0000
parents 480d9e9d156b
children ea5e944f447d
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f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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1 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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2 <description>Submission of (meta)data to the European Nucleotide Archive (ENA)</description>
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3 <macros>
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f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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4 <token name="@TOOL_VERSION@">0.7.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <import>samples_macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement>
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10 </requirements>
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11 <stdio>
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12 <regex match="Oops" source="stderr" level="fatal"/>
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13 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
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14 </stdio>
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15 <command detect_errors="exit_code"><![CDATA[
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16 mkdir ./submission_files;
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17 #set $studies_table_path = './submission_files/studies.tsv'
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18 #set $samples_table_path = './submission_files/samples.tsv'
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19 #set $experiments_table_path = './submission_files/experiments.tsv'
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20 #set $runs_table_path = './submission_files/runs.tsv'
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22 #set $studies_table_path_updated = './submission_files/studies_updated.tsv'
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23 #set $samples_table_path_updated = './submission_files/samples_updated.tsv'
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24 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv'
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25 #set $runs_table_path_updated = './submission_files/runs_updated.tsv'
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27 #set working_dir = os.getcwd()
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28 #if $action_options.input_format_conditional.input_format == "build_tables":
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29 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
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30 #end if
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32 credentials_path='test_fake_path';
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33 echo "username: test_user" > \$credentials_path;
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34 echo "password: test_password" >> \$credentials_path;
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35
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36
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37 #if $action_options.input_format_conditional.input_format == "build_tables":
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38 cp $studies_table_path $studies_table_out &&
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39 cp $samples_table_path $samples_table_out &&
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40 cp $experiments_table_path $experiments_table_out &&
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41 cp $runs_table_path $runs_table_out &&
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42 #end if
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43 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
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44 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
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45 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
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46 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
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47 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
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48 #end if
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49 #if $action_options.input_format_conditional.input_format == "excel_tables":
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50 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
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51 #end if
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52 #if $action_options.input_format_conditional.input_format == "isa_json":
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53 ln -s '$action_options.input_format_conditional.isa_json_file' ./isa_json_input.json &&
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54 #end if
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55 #if $action_options.test_submit_parameters.dry_run == "False":
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56 webin_id=`grep 'username' $credentials`;
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57 if [ "\$webin_id" = "" ]; then
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58 ## No credentials in user defined preferences
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59 ## Fallback to global defined credentials (if exist)
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60 #import os
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61 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
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62 credentials_path=\${GALAXY_ENA_SECRETS};
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63 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
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64 if [ "\$webin_id" = "" ]; then
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65 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
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66 exit 1;
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67 fi;
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68 #else:
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69 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
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70 exit 1;
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71 #end if
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72 else
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73 credentials_path='$credentials';
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74 fi;
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75 #end if
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76
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77
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78 ## create the list of files to upload and make the symlinks
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79 #import re
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80 #set $files_to_upload = list()
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81 #if $action_options.input_format_conditional.input_format == "build_tables":
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82 #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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parents:
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83 #for $sample in $study.rep_sample:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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84 #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:
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85 #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:
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86 #for $file in $run.upload_files:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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87 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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parents: 9
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88 #if $action_options.input_format_conditional.add_extension == "True":
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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89 #set $extension = '.fastq'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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90 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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91 #set $extension = ''
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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92 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
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93 #if $file.is_of_type('fastq', 'fastqsanger'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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94 ## compression output is defined as safename_reads_file so no need to symlink
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
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95 #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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96 gzip -c '$file' > $safename_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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97 #else:
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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parents: 9
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98 #if $action_options.input_format_conditional.add_extension == "True":
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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99 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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100 #set $compression = '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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101 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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102 #set $compression = '.bz2'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
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103 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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104 #set $safename_reads_file = $safename_reads_file + $extension + $compression
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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105 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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106 ln -s '$file' $safename_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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107 #end if
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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108 $files_to_upload.append(str($safename_reads_file))
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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109 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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110 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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111 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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112 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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113 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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114 #else:
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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115 #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"
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116 #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"
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117 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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118 ## Always need to add .fastq + compression suffix because the name is based on the pair name which has no extensions
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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119 #if $pair.forward.is_of_type('fastq', 'fastqsanger'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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120 ## compress the file, no need to create the link then
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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121 ## always add the compression suffix (.gz)
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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122 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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123 gzip -c '$file' > $safename_fwd_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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124 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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125 #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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126 #set $compression = '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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127 #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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128 #set $compression = '.bz2'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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129 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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130 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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131 ln -s '$pair.forward' $safename_fwd_reads_file &&
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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132 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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133
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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134 #if $pair.reverse.is_of_type('fastq', 'fastqsanger'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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135 ## compress the file, no need to create the link then
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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136 #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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137 gzip -c '$file' > $safename_rev_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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138 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
139 #if $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
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140 #set $compression = '.bz2'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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diff changeset
141 #elif $pair.reverse.is_of_type('fastqsanger.gz', 'fastq.gz'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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142 #set $compression = '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
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143 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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144 #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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145 ln -s '$pair.reverse' $safename_rev_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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146 #end if
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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147 $files_to_upload.append(str($safename_fwd_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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148 $files_to_upload.append(str($safename_rev_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
149 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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parents: 0
diff changeset
150 #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
151 #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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152 #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"
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153 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
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154 #if $file.is_of_type('fastq', 'fastqsanger'):
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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155 ## always compress add the gz extension
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
156 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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157 #set $safename_reads_file = $safename_reads_file + '.fastq.gz'
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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158 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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159 #set $safename_reads_file = $safename_reads_file + '.gz'
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
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160 #end if
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
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161 gzip -c '$file' > $safename_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
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162 #else
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
163 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
164 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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165 #set $extension = '.fastq.gz'
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
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166 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
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167 #set $extension = '.fastq.bz2'
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168 #end if
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169 #set $safename_reads_file = $safename_reads_file + $extension
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170 #end if
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171 ln -s '$file' $safename_reads_file &&
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172 #end if
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173 $files_to_upload.append(str($safename_reads_file))
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174 #end for
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175 #end if
0
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176 #end if
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177
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178 ena-upload-cli
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179 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy'
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180 --action '$action_options.action'
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181 --center '$action_options.test_submit_parameters.center'
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182 --secret \${credentials_path}
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183 --data
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184 #for $dataset in $files_to_upload:
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185 '$dataset'
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186 #end for
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187 #if $action_options.test_submit_parameters.dry_run == "True":
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188 --draft
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189 #end if
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190 #if $action_options.input_format_conditional.input_format == "excel_tables":
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191 --xlsx ./xlsx_input.xlsx
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192 #elif $action_options.input_format_conditional.input_format == "user_generated_tables" or $action_options.input_format_conditional.input_format == "build_tables":
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193 --experiment '$experiments_table_path'
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194 --study '$studies_table_path'
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195 --run '$runs_table_path'
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196 --sample '$samples_table_path'
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197 #elif $action_options.input_format_conditional.input_format == "isa_json":
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198 --isa_json ./isa_json_input.json
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199 --isa_assay_stream '$isa_assay_stream'
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200 #end if
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201 #if $action_options.input_format_conditional.input_format == "build_tables":
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202 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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203 --checklist ERC000033
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204 #end if
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205 #elif $action_options.input_format_conditional.input_format == "isa_json":
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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206 --checklist ERC000011
0
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207 #else:
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208 --checklist $action_options.input_format_conditional.checklist_id
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209 #end if
10
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210 #if $action_options.test_submit_parameters.submit_dev == "True":
0
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211 -d
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212 #end if
11
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213 >> '$output';
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214
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215
10
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216 #if $action_options.test_submit_parameters.dry_run == "False":
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217 echo -e 'center_name\t$action_options.test_submit_parameters.center' >> '$output';
1
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218 echo -e 'action_option\t$action_options.action' >> '$output';
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219 #end if
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220
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221 ## copy updated files
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222 #if $action_options.input_format_conditional.input_format == "excel_tables" or $action_options.input_format_conditional.input_format == "isa_json":
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223 ## for the excel/ISA json input case, copy the upload-cli generated tables to the output files
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224 ## this applies for both draft and real submissions
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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225 cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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226 cp './ENA_template_sample_updated.tsv' $samples_table_out;
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227 cp './ENA_template_study_updated.tsv' $studies_table_out;
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228 cp './ENA_template_run_updated.tsv' $runs_table_out;
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229 #else
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230 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
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231 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
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232 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
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233 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
0
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234 #end if
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235
7
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236 python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output;
0
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237 ]]></command>
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238 <configfiles>
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239 <configfile name="credentials"><![CDATA[
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240 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
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241 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
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242 #if $webin_id != "":
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243 username: "$webin_id"
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244 password: "$password"
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245 #end if
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246 ]]></configfile>
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247 <configfile name="studies_json">
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248 #import json
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249 #import re
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250 #if $action_options.input_format_conditional.input_format == "build_tables":
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251 #set $files_to_upload = list()
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252 #set $studies = list()
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253 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
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254 #set samples = list()
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255 #for $sample in $study.rep_sample:
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256 #set experiments = list()
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257 #for $experiment in $sample.rep_experiment:
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258 #set runs = list()
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259 #for $run in $experiment.rep_runs:
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260 #set run_files = list()
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261 #for $file in $run.upload_files:
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262 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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263 $run_files.append(str($safename_reads_file))
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264 #end for
1
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265 $runs.append((str($run.run_base_name),$run_files))
0
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266 #end for
1
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267
0
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268 $experiments.append({'title':str($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})
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269 #end for
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270 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
0
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271 $samples.append({'title':str($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})
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272 #else:
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273 $samples.append({'title':str($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($sample.geo_location_country),'experiments':$experiments})
0
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274 #end if
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275 #end for
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276 $studies.append({'title':str($study.study_title),'type':str($study.study_type),'abstract':str($study.study_abstract),'pubmed_id':str($study.study_pubmed_id),'samples':$samples})
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277 #end for
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278 #echo $json.dumps($studies)
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279 #end if
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280 </configfile>
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281 </configfiles>
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282 <inputs>
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283 <conditional name="action_options">
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284 <param name="action" type="select" label="Action to execute">
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285 <option value="add" selected="True">Add new (meta)data</option>
0
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286 <option value="modify">Modify metadata</option>
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287 </param>
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288 <when value="add">
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289 <param name="test_submit" type="hidden" value="False" />
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290 <expand macro="table_inputs_macro" />
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291 <expand macro="test_submit_section"/>
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292 </when>
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293 <when value="modify">
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294 <param name="test_submit" type="hidden" value="False" />
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295 <expand macro="table_inputs_macro" />
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296 <expand macro="test_submit_section"/>
0
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297 </when>
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298 </conditional>
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299 </inputs>
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300 <outputs>
1
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301 <data name="output" format="txt" label="ENA submission receipt"/>
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302 <data name="studies_table_out" format="tabular" label="Studies table">
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303 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
0
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304 </data>
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305 <data name="samples_table_out" format="tabular" label="Samples table">
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306 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
0
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307 </data>
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308 <data name="experiments_table_out" format="tabular" label="Experiments table">
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309 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
0
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310 </data>
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311 <data name="runs_table_out" format="tabular" label="Runs table">
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312 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"</filter>
0
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313 </data>
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314 </outputs>
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315 <tests>
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316 <!--Test 1: excel input of VIRAL samples -->
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317 <test expect_num_outputs="5">
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318 <conditional name="action_options">
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319 <param name="action" value="add"/>
1
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320 <section name="test_submit_parameters">
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321 <param name="center" value="Some research center"/>
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322 <param name="submit_dev" value="False" />
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323 <param name="dry_run" value="True" />
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324 </section>
0
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325 <conditional name="input_format_conditional">
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326 <param name="input_format" value="excel_tables"/>
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327 <param name="checklist_id" value="ERC000033"/>
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328 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
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329 <conditional name="run_input_format_conditional">
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330 <param name="add_extension" value="False"/>
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331 <param name="run_input_format" value="multiple_selection_list"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
332 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
333 </conditional>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
334 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
335 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
336 <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
337 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
338 <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
339 <has_n_columns n="17"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
340 <has_line_matching expression="alias\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\taccession\tsubmission_date\tstatus"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
341 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
342 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
343 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
344 <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
345 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
346 <has_n_lines n="2"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
347 <has_n_columns n="7"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
348 <has_line_matching expression="SARS-CoV-2_genomes_01\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(.*)"/>
0
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 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
351 <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
352 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
353 <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
354 <has_n_columns n="18"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
355 </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
356 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
357 <output name="runs_table_out">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
358 <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
359 <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
360 <has_n_columns n="8"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
361 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
362 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
363 </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
364 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
365 </test>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
366 <!--Test 2: excel input of VIRAL samples with extended columns-->
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
367 <test expect_num_outputs="5">
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
368 <conditional name="action_options">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
369 <param name="action" value="add"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
370 <section name="test_submit_parameters">
11
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
371 <param name="center" value="Some research center"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
372 <param name="submit_dev" value="False" />
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
373 <param name="dry_run" value="True" />
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
374 </section>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
375 <conditional name="input_format_conditional">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
376 <param name="input_format" value="excel_tables"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
377 <param name="checklist_id" value="ERC000033"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
378 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
379 <conditional name="run_input_format_conditional">
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
380 <param name="add_extension" value="False"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
381 <param name="run_input_format" value="multiple_selection_list"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
382 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
383 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
384 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
385 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
386 <output name="experiments_table_out">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
387 <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
388 <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
389 <has_n_columns n="17"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
390 <has_line_matching expression="alias\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\taccession\tsubmission_date\tstatus"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
391 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
392 </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
393 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
394 <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
395 <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
396 <has_n_lines n="2"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
397 <has_n_columns n="7"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
398 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
399 <has_line_matching expression="SARS-CoV-2_genomes_01\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(.*)"/>
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
400 </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
401 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
402 <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
403 <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
404 <has_n_lines n="5"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
405 <has_n_columns n="43"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
406 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
407 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
408 <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
409 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
410 <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
411 <has_n_columns n="8"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
412 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
413 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
414 </assert_contents>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
415 </output>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
416 <output name="output">
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
417 <assert_contents>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
418 <has_line_matching expression="YAML -------------"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
419 <has_line_matching expression="ENA_experiment:"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
420 <has_line_matching expression="ENA_sample:"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
421 <has_line_matching expression="ENA_study:"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
422 <has_line_matching expression="ENA_run:"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
423 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
424 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
425 </test>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
426 <!--Test 3: excel input of NON-VIRAL samples-->
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
427 <test expect_num_outputs="5">
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
428 <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
429 <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
430 <section name="test_submit_parameters">
11
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
431 <param name="center" value="Some research center"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
432 <param name="submit_dev" value="False" />
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
433 <param name="dry_run" value="True" />
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
434 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
435 <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
436 <param name="input_format" value="excel_tables"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
437 <param name="checklist_id" value="ERC000011"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
438 <param name="xlsx_file" value="metadata_test_nonviral_1_run.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
439 <conditional name="run_input_format_conditional">
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
440 <param name="add_extension" value="True"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
441 <param name="run_input_format" value="multiple_selection_list"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
442 <param name="data" value="sample_no_extension"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
443 </conditional>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
444 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
445 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
446 <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
447 <assert_contents>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
448 <has_n_lines n="2"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
449 <has_n_columns n="17"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
450 <has_line_matching expression="alias\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\taccession\tsubmission_date\tstatus"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
451 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
452 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
453 <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
454 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
455 <has_n_lines n="2"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
456 <has_n_columns n="7"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
457 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
458 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
459 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
460 <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
461 <assert_contents>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
462 <has_n_lines n="2"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
463 <has_n_columns n="10"/>
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
464 <has_line_matching expression="s_20201007_026\tC026\tSaccharomyces cerevisiae\tSample from beer\t2020-03-25\tAntarctica\t\t\tADDED\t"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
465 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
466 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
467 <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
468 <assert_contents>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
469 <has_n_lines n="2"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
470 <has_n_columns n="8"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
471 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
472 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
473 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
474 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
475 </test>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
476 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
477 <test expect_failure="True">
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
478 <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
479 <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
480 <section name="test_submit_parameters">
11
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
481 <param name="center" value="Some research center"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
482 <param name="submit_dev" value="False" />
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
483 <param name="dry_run" value="False" />
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
484 </section>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
485 <conditional name="input_format_conditional">
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
486 <param name="add_extension" value="True"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
487 <param name="input_format" value="excel_tables"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
488 <param name="checklist_id" value="ERC000011"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
489 <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
490 <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
491 <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
492 <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
493 <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
494 <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
495 <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
496 <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
497 <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
498 </collection>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
499 </element>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
500 </collection>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
501 </param>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
502 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
503 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
504 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
505 <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
506 <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
507 <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
508 <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
509 </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
510 </test>
11
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iuc
parents: 10
diff changeset
511 <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
10
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iuc
parents: 9
diff changeset
512 <test expect_failure="True">
8
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
513 <conditional name="action_options">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
514 <param name="action" value="add"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
515 <section name="test_submit_parameters">
11
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parents: 10
diff changeset
516 <param name="center" value="Some research center"/>
10
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iuc
parents: 9
diff changeset
517 <param name="submit_dev" value="False" />
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
518 <param name="dry_run" value="False" />
8
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
519 </section>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
520 <conditional name="input_format_conditional">
10
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parents: 9
diff changeset
521 <param name="add_extension" value="True"/>
8
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
522 <param name="input_format" value="excel_tables"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
523 <param name="checklist_id" value="ERC000011"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
524 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
525 <conditional name="run_input_format_conditional">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
526 <param name="run_input_format" value="paired_list"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
527 <param name="paired_end_collection">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
528 <collection type="list:paired">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
529 <element name="paired_run_name">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
530 <collection type="paired">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
531 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" />
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
532 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" />
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
533 </collection>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
534 </element>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
535 </collection>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
536 </param>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
537 </conditional>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
538 </conditional>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
539 </conditional>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
540 <assert_command>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
541 <has_text_matching expression="ena-upload-cli"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
542 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
543 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
544 </assert_command>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
545 </test>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
546 <!--Test 5: build tables from user input fields NON-VIRAL samples-->
10
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iuc
parents: 9
diff changeset
547 <test expect_num_outputs="5">
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
548 <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
549 <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
550 <section name="test_submit_parameters">
11
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parents: 10
diff changeset
551 <param name="center" value="Some research center"/>
10
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iuc
parents: 9
diff changeset
552 <param name="submit_dev" value="False" />
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
553 <param name="dry_run" value="True" />
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
554 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
555 <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
556 <param name="input_format" value="build_tables"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
557 <param name="add_extension" 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
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 <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
565 <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
566 <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
567 <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
568 <param name="scientific_name" value="Test Sample scientific name"/>
7
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parents: 6
diff changeset
569 <param name="tax_id" value="2697049"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
570 <param name="collection_date" value="2020"/>
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
571 <param name="geo_location_country" value="Belgium"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
572 <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
573 <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
574 <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
575 <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
576 <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
577 <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
578 <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
579 <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
580 <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
581 <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
582 <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
583 <repeat name="rep_runs">
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
584 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger.gz"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
585 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
586 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
587 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
588 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
589 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
590 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
591 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
592 <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
593 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
594 <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
595 <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
596 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
597 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
598 <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
599 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
600 <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
601 <has_n_columns n="8"/>
9
a62c4a11a67d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6770d277b4136b4068293c4260022d4ae33b2379
iuc
parents: 8
diff changeset
602 <has_line_matching expression="alias\tstatus\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\taccession\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
603 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
604 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
605 <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
606 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
607 <has_n_lines n="2"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
608 <has_n_columns n="10"/>
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_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
610 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
611 <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
612 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
613 <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
614 <has_n_columns n="8"/>
9
a62c4a11a67d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6770d277b4136b4068293c4260022d4ae33b2379
iuc
parents: 8
diff changeset
615 <has_line_matching expression="alias\tstatus\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tfile_checksum"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
616 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
617 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
618 </test>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
619 <!--Test 6: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
620 also tests compression of uncompressed inputs and adding the .gz suffix -->
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
621 <test expect_failure="False" expect_num_outputs="5">
0
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="action_options">
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="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
624 <section name="test_submit_parameters">
11
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
625 <param name="center" value="Some research center"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
626 <param name="submit_dev" value="True" />
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
627 <param name="dry_run" value="True" />
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
628 </section>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
629 <param name="test_submit" value="True"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
630 <conditional name="input_format_conditional">
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
631 <param name="add_extension" 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
632 <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
633 <conditional name="conditional_viral_metadata">
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
634 <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
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 <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
642 <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
643 <param name="scientific_name" value="Test Sample scientific name"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
644 <param name="tax_id" value="2697049"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
645 <param name="collection_date" value="2020"/>
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
646 <param name="geo_location_country" value="Belgium"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
647 <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
648 <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
649 <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
650 <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
651 <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
652 <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
653 <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
654 <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
655 <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
656 <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
657 <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
658 <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
659 <param name="run_base_name" value="run_from_hospital_X"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
660 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
0
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 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
663 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
664 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
665 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
666 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
667 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
668 <assert_command>
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="ena-upload-cli"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
670 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
671 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
4
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672 <not_has_text text="modify" />
0
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673 </assert_command>
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674 </test>
10
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675 <!--Test 7: viral submission - User input metadata - Add extension = False-->
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676 <test expect_failure="False" expect_num_outputs="5">
0
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diff changeset
677 <conditional name="action_options">
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678 <param name="action" value="add"/>
1
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679 <section name="test_submit_parameters">
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680 <param name="center" value="Some research center"/>
10
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681 <param name="submit_dev" value="False" />
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682 <param name="dry_run" value="True" />
1
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683 </section>
0
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684 <param name="test_submit" value="True"/>
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685 <conditional name="input_format_conditional">
10
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686 <param name="add_extension" value="False"/>
4
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687 <param name="input_format" value="build_tables"/>
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688 <conditional name="conditional_viral_metadata">
10
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689 <param name="viral_sample" value="True"/>
4
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690 <repeat name="rep_study">
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691 <param name="study_title" value="Test study title"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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692 <param name="study_abstract" value="Test study abstract"/>
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693 <param name="study_type" value="Epigenetics"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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694 <param name="study_pubmed_id" value="Test study pubmedID"/>
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695 <repeat name="rep_sample">
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696 <param name="sample_title" value="Test Sample title"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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diff changeset
697 <param name="sample_description" value="Test Sample description"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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diff changeset
698 <param name="scientific_name" value="Test Sample scientific name"/>
7
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parents: 6
diff changeset
699 <param name="tax_id" value="2697049"/>
4
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diff changeset
700 <param name="collection_date" value="2020"/>
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diff changeset
701 <param name="geo_location_country" value="Belgium"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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diff changeset
702 <param name="host_common_name" value="Human"/>
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diff changeset
703 <param name="host_subject_id" value="Patient_001"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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diff changeset
704 <param name="host_health_state" value="healthy"/>
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diff changeset
705 <param name="host_sex" value="female"/>
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parents: 3
diff changeset
706 <param name="host_scientific_name" value="homo sapiens"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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diff changeset
707 <param name="collector_name" value="John The Collector"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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diff changeset
708 <param name="collecting_institution" value="Hospital 01"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
709 <param name="isolate" value="sample_001"/>
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parents: 3
diff changeset
710 <repeat name="rep_experiment">
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parents: 3
diff changeset
711 <param name="experiment_title" value="Test experiment title"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
712 <param name="experiment_design" value="Test experiment design description"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
713 <param name="library_strategy" value="CTS"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
714 <param name="library_source" value="GENOMIC"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
715 <param name="library_selection" value="PCR"/>
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parents: 3
diff changeset
716 <param name="library_layout" value="SINGLE"/>
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diff changeset
717 <param name="insert_size" value="150"/>
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parents: 3
diff changeset
718 <param name="library_construction_protocol" value="Test library construction"/>
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parents: 3
diff changeset
719 <param name="platform" value="ILLUMINA"/>
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parents: 3
diff changeset
720 <param name="instrument_model" value="Illumina HiSeq 4000"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
721 <repeat name="rep_runs">
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parents: 3
diff changeset
722 <param name="run_base_name" value="run_from_hospital_X"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
723 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
724 </repeat>
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parents: 3
diff changeset
725 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
726 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
727 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
728 </conditional>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
729 </conditional>
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parents: 3
diff changeset
730 </conditional>
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iuc
parents: 3
diff changeset
731 <assert_command>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
732 <has_text_matching expression="ena-upload-cli"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
733 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
734 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
735 <has_text_matching expression="--checklist ERC000033"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
736 </assert_command>
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parents: 3
diff changeset
737 </test>
10
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parents: 9
diff changeset
738 <!--Test 8: modify option and auto compression - viral submission - User input metadata-->
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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parents: 9
diff changeset
739 <test expect_failure="False" expect_num_outputs="5">
4
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iuc
parents: 3
diff changeset
740 <conditional name="action_options">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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parents: 3
diff changeset
741 <param name="action" value="modify"/>
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parents: 3
diff changeset
742 <section name="test_submit_parameters">
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parents: 10
diff changeset
743 <param name="center" value="Some research center"/>
10
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parents: 9
diff changeset
744 <param name="submit_dev" value="False" />
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iuc
parents: 9
diff changeset
745 <param name="dry_run" value="True" />
4
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parents: 3
diff changeset
746 </section>
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parents: 3
diff changeset
747 <param name="test_submit" value="True"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
748 <conditional name="input_format_conditional">
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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parents: 9
diff changeset
749 <param name="add_extension" value="False"/>
0
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iuc
parents:
diff changeset
750 <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
751 <conditional name="conditional_viral_metadata">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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parents:
diff changeset
752 <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
753 <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
754 <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"
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parents:
diff changeset
755 <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
756 <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
757 <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
758 <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
759 <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
760 <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
761 <param name="scientific_name" value="Test Sample scientific name"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
762 <param name="tax_id" value="2697049"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
763 <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
764 <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
765 <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
766 <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
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 <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
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 <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
784 <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
785 <param name="run_base_name" value="run_from_hospital_X"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
786 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
787 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
788 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
789 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
790 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
791 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
792 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
793 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
794 <assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
795 <has_text_matching expression="ena-upload-cli"/>
10
480d9e9d156b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents: 9
diff changeset
796 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
797 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
798 <has_text_matching expression="--checklist ERC000033"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
799 <not_has_text text="add" />
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
800 </assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
801 </test>
11
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
802 <!--Test 9: isa JSON input of NON-VIRAL samples-->
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
803 <test expect_num_outputs="5">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
804 <conditional name="action_options">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
805 <param name="action" value="add"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
806 <section name="test_submit_parameters">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
807 <param name="center" value="Some research center"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
808 <param name="submit_dev" value="True" />
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
809 <param name="dry_run" value="True" />
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
810 </section>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
811 <conditional name="input_format_conditional">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
812 <param name="input_format" value="isa_json"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
813 <param name="isa_json_file" value="simple_test_case_v2.json"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
814 <param name="isa_assay_stream" value="Ena stream 1"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
815 <conditional name="run_input_format_conditional">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
816 <param name="add_extension" value="False"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
817 <param name="run_input_format" value="multiple_selection_list"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
818 <param name="data" value="ENA_TEST1.R1.fastq.gz,ENA_TEST2.R1.fastq.gz,ENA_TEST2.R2.fastq.gz"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
819 </conditional>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
820 </conditional>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
821 </conditional>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
822 <output name="experiments_table_out">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
823 <assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
824 <has_n_lines n="4"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
825 <has_n_columns n="17"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
826 <has_line_matching expression="alias\tstudy_alias\tsample_alias\tlibrary_name\ttitle\taccession\tsubmission date\tstatus\tdesign_description\tlibrary_source\tlibrary_strategy\tlibrary_selection\tlibrary_layout\tinsert_size\tplatform\tinstrument_model\tsubmission_date"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
827 </assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
828 </output>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
829 <output name="studies_table_out">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
830 <assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
831 <has_n_lines n="2"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
832 <has_n_columns n="9"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
833 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\tnew_study_type\tpubmed_id\taccession\tsubmission_date\tstatus"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
834 </assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
835 </output>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
836 <output name="samples_table_out">
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
837 <assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
838 <has_n_lines n="3"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
839 <has_n_columns n="11"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
840 </assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
841 </output>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
iuc
parents: 10
diff changeset
842 <output name="runs_table_out">
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843 <assert_contents>
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844 <has_n_lines n="4"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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845 <has_n_columns n="10"/>
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846 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_type\tfile checksum\taccession\tsubmission date\tstatus\tsubmission_date\tfile_checksum"/>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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847 </assert_contents>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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848 </output>
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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849 </test>
0
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850 </tests>
11
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851 <help><![CDATA[This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli. The input metadata can be submitted following the tabular format of the templates or their excel spreadsheet equivalent in https://github.com/ELIXIR-Belgium/ENA-metadata-templates. This template repo provides ready to use sheets for every ENA sample checklist and is automatically updated.
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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852
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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853 .. class:: warningmark
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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854
f803a68fc9e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
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855 The ENA upload tool won't work unless you have provided an ENA Webin ID in User > Preferences > Manage Information > ENA Webin account details.]]></help>
0
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856 <citations>
10
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857 <citation type="doi">doi:10.1093/bioinformatics/btab421</citation>
0
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858 </citations>
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859 </tool>