Mercurial > repos > iuc > ena_upload

annotate ena_upload.xml @ 8:d147d6455873 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
author iuc
date Wed, 04 May 2022 17:06:42 +0000
parents 6f6537780379
children a62c4a11a67d
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26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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1 <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT">
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2 <macros>
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3 <token name="@VERSION@">0.6.0</token>
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4 <import>samples_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
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8 </requirements>
1
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9 <stdio>
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10 <regex match="Oops" source="stderr" level="fatal"/>
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iuc
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11 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/>
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
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14 mkdir ./submission_files;
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15 #set $studies_table_path = './submission_files/studies.tsv'
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16 #set $samples_table_path = './submission_files/samples.tsv'
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17 #set $experiments_table_path = './submission_files/experiments.tsv'
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18 #set $runs_table_path = './submission_files/runs.tsv'
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20 #set $studies_table_path_updated = './submission_files/studies_updated.tsv'
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21 #set $samples_table_path_updated = './submission_files/samples_updated.tsv'
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22 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv'
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23 #set $runs_table_path_updated = './submission_files/runs_updated.tsv'
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24
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25 #set working_dir = os.getcwd()
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26 #if $action_options.input_format_conditional.input_format == "build_tables":
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27 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
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28 #end if
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30 credentials_path='test_fake_path';
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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31 echo "username: test_user" > \$credentials_path;
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32 echo "password: test_password" >> \$credentials_path;
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34
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35 #if $action_options.input_format_conditional.input_format == "build_tables":
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36 cp $studies_table_path $studies_table_out &&
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37 cp $samples_table_path $samples_table_out &&
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38 cp $experiments_table_path $experiments_table_out &&
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39 cp $runs_table_path $runs_table_out &&
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40 #end if
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41 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
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42 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
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43 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
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44 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
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45 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
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46 #end if
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47 #if $action_options.input_format_conditional.input_format == "excel_tables":
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48 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
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49 #end if
1
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50 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
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51 webin_id=`grep 'username' $credentials`;
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52 if [ "\$webin_id" = "" ]; then
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53 ## No credentials in user defined preferences
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54 ## Fallback to global defined credentials (if exist)
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55 #import os
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56 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
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57 credentials_path=\${GALAXY_ENA_SECRETS};
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58 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
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59 if [ "\$webin_id" = "" ]; then
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60 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
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61 exit 1;
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62 fi;
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63 #else:
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64 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
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65 exit 1;
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66 #end if
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67 else
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68 credentials_path='$credentials';
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69 fi;
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70 #end if
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71
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72
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73 ## create the list of files to upload and make the symlinks
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74 #import re
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75 #set $files_to_upload = list()
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76 #if $action_options.input_format_conditional.input_format == "build_tables":
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77 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
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78 #for $sample in $study.rep_sample:
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79 #for $experiment in $sample.rep_experiment:
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80 #for $run in $experiment.rep_runs:
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81 #for $file in $run.upload_files:
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82 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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83 #if $action_options.input_format_conditional.add_extension == "true":
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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84 #set $extension = '.fastq'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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85 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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86 #set $extension = ''
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87 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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88 #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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89 ## 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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90 #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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91 gzip -c '$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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92 #else:
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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93 #if $action_options.input_format_conditional.add_extension == "true":
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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94 #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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95 #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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96 #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"
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97 #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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98 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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99 #set $safename_reads_file = $safename_reads_file + $extension + $compression
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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100 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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101 ln -s '$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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102 #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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103 $files_to_upload.append(str($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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104 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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105 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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106 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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107 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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108 #end for
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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109 #else:
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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110 #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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111 #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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112 #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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113 ## 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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114 #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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115 ## 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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116 ## 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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117 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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118 gzip -c '$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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119 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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120 #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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121 #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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122 #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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123 #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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124 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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125 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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126 ln -s '$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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127 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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128
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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129 #if $pair.reverse.is_of_type('fastq', 'fastqsanger'):
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130 ## 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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131 #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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132 gzip -c '$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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133 #else
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('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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135 #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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136 #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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137 #set $compression = '.gz'
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138 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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139 #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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140 ln -s '$pair.reverse' $safename_rev_reads_file &&
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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141 #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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142 $files_to_upload.append(str($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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143 $files_to_upload.append(str($safename_rev_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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144 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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145 #end if
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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146 #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"
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147 #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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148 #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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149 #if $file.is_of_type('fastq', 'fastqsanger'):
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150 ## always compress add the gz extension
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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151 #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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152 #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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153 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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154 #set $safename_reads_file = $safename_reads_file + '.gz'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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155 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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156 gzip -c '$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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157 #else
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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158 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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159 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
7
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160 #set $extension = '.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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161 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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162 #set $extension = '.fastq.bz2'
4
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163 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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164 #set $safename_reads_file = $safename_reads_file + $extension
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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165 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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166 ln -s '$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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167 #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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diff changeset
168 $files_to_upload.append(str($safename_reads_file))
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
169 #end for
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
170 #end if
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
171 #end if
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
172
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
173 #if $action_options.action == "add":
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
174 ena-upload-cli
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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parents:
diff changeset
175 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
176 --action '$action_options.action'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
177 --center '$action_options.center'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
178 --secret \${credentials_path}
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
179 --data
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
180 #for $dataset in $files_to_upload:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
181 '$dataset'
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
182 #end for
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
183 #if $action_options.test_submit_parameters.dry_run == "true":
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
184 --draft
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
185 #end if
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
186 #if $action_options.input_format_conditional.input_format != "excel_tables":
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
187 --experiment '$experiments_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
188 --study '$studies_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
189 --run '$runs_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
190 --sample '$samples_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
191 #else
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
192 --xlsx ./xlsx_input.xlsx
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
193 #end if
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
194 --action add
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
195 #if $action_options.input_format_conditional.input_format == "user_generated_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
196 --checklist $action_options.input_format_conditional.checklist_id
0
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
197 #else:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
198 #if $action_options.input_format_conditional.input_format == "build_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
199 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "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
200 --checklist ERC000033
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
201 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
202 #else:
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
203 --checklist $action_options.input_format_conditional.checklist_id
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
204 #end if
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
205 #end if
8
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
206 #if $action_options.idempotent == "true":
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
207 --auto_action
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
208 #end if
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
209 #if $action_options.test_submit_parameters.submit_dev == "true":
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
210 -d
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
211 #end if
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
212 >> '$output';
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
213 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
214
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
215
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
216
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
217 #if $action_options.action == "modify":
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
218 ena-upload-cli
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
219 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
220 --action '$action_options.action'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
221 --center '$action_options.center'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
222 --secret \${credentials_path}
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
223 --data
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
224 #for $dataset in $files_to_upload:
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
225 '$dataset'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
226 #end for
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
227 #if $action_options.test_submit_parameters.dry_run == "true":
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
228 --draft
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
229 #end if
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
230 #if $action_options.input_format_conditional.input_format != "excel_tables":
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
231 --experiment '$experiments_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
232 --study '$studies_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
233 --run '$runs_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
234 --sample '$samples_table_path'
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
235 #else
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
236 --xlsx ./xlsx_input.xlsx
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
237 --auto_action
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
238 #end if
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
239 --action 'modify'
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
240 #if $action_options.input_format_conditional.input_format == "user_generated_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
241 --checklist $action_options.input_format_conditional.checklist_id
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
242 #else:
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
243 #if $action_options.input_format_conditional.input_format == "build_tables":
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
244 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
245 --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
246 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
247 #else:
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
248 --checklist $action_options.input_format_conditional.checklist_id
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
249 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
250 #end if
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
251 >> '$output';
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
252 #end if
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
253
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
254 #if $action_options.test_submit_parameters.dry_run == "false":
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
255 echo -e 'center_name\t$action_options.center' >> '$output';
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
256 echo -e 'action_option\t$action_options.action' >> '$output';
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
257 #end if
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
258
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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259 ## copy updated files
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260 #if $action_options.input_format_conditional.input_format == "excel_tables":
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261 ## for the excel input case, copy the upload-cli generated tables to the output files
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262 ## this applies for both draft and real submissions
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263 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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264 cp './ENA_template_sample_updated.tsv' $samples_table_out;
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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265 cp './ENA_template_study_updated.tsv' $studies_table_out;
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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266 cp './ENA_template_run_updated.tsv' $runs_table_out;
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267 #else
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268 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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269 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
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270 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
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271 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
0
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272 #end if
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273
7
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274 python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output;
0
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275 ]]></command>
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276 <configfiles>
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277 <configfile name="credentials"><![CDATA[
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278 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
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279 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
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280 #if $webin_id != "":
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281 username: "$webin_id"
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282 password: "$password"
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283 #end if
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284 ]]></configfile>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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285 <configfile name="studies_json">
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286 #import json
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287 #import re
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288 #if $action_options.input_format_conditional.input_format == "build_tables":
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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289 #set $files_to_upload = list()
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290 #set $studies = list()
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291 #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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292 #set samples = list()
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293 #for $sample in $study.rep_sample:
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294 #set experiments = list()
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295 #for $experiment in $sample.rep_experiment:
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296 #set runs = list()
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297 #for $run in $experiment.rep_runs:
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298 #set run_files = list()
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299 #for $file in $run.upload_files:
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300 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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301 $run_files.append(str($safename_reads_file))
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302 #end for
1
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303 $runs.append((str($run.run_base_name),$run_files))
0
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304 #end for
1
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305
0
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306 $experiments.append({'title':str($experiment.experiment_title),'experiment_design':str($experiment.experiment_design),'library_strategy':str($experiment.library_strategy),'library_source':str($experiment.library_source),'library_selection':str($experiment.library_selection),'library_layout':str($experiment.library_layout),'insert_size':str($experiment.insert_size),'library_construction_protocol':str($experiment.library_construction_protocol),'platform':str($experiment.platform),'instrument_model':str($experiment.instrument_model),'runs':$runs})
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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307 #end for
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308 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
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309
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310 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'host_common_name':str($sample.host_common_name),'host_subject_id':str($sample.host_subject_id),'host_health_state':str($sample.host_health_state),'host_sex':str($sample.host_sex),'host_scientific_name':str($sample.host_scientific_name),'collector_name':str($sample.collector_name),'collecting_institution':str($sample.collecting_institution),'isolate':str($sample.isolate),'experiments':$experiments})
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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311 #else:
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312
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313 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'experiments':$experiments})
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314 #end if
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315 #end for
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316 $studies.append({'title':str($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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317 #end for
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318 #echo $json.dumps($studies)
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319 #end if
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320 </configfile>
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321 </configfiles>
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322 <inputs>
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323 <conditional name="action_options">
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324 <param name="action" type="select" label="Action to execute">
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325 <option value="add" selected="True">Add new data</option>
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326 <option value="modify">Modify metadata</option>
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327 </param>
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328 <when value="add">
8
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329 <param type="boolean" name="idempotent" checked="False" label="Idempotent submissions: only add the elements that were not submitted before" help="NOTE: this feature is based on a beta parameter of the CLI that checks the remote ENA repository for entries using the alias. This remote detection can have false positives, i.e assumes that it's present in the repository but it's not"/>
1
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330 <expand macro="test_submit_section"/>
0
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331 <param name="test_submit" type="hidden" value="False" />
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332 <expand macro="table_inputs_macro" />
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333 </when>
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334 <when value="modify">
1
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335 <expand macro="test_submit_section"/>
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336 <param name="test_submit" type="hidden" value="False" />
0
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337 <expand macro="table_inputs_macro" />
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338 </when>
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339 </conditional>
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
340 </inputs>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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341 <outputs>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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342 <data name="output" format="txt" label="ENA submission receipt"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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343 <data name="studies_table_out" format="tabular" label="Studies table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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344 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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345 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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346 <data name="samples_table_out" format="tabular" label="Samples table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
347 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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348 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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349 <data name="experiments_table_out" format="tabular" label="Experiments table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
350 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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351 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
352 <data name="runs_table_out" format="tabular" label="Runs table">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
353 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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354 </data>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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355 </outputs>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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356 <tests>
7
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357 <!--Test 1: excel input of VIRAL samples -->
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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358 <test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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359 <conditional name="action_options">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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360 <param name="action" value="add"/>
1
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parents: 0
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361 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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parents: 0
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362 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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diff changeset
363 <param name="dry_run" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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parents: 0
diff changeset
364 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
365 <conditional name="input_format_conditional">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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366 <param name="input_format" value="excel_tables"/>
7
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parents: 6
diff changeset
367 <param name="checklist_id" value="ERC000033"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
368 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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parents: 0
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369 <conditional name="run_input_format_conditional">
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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370 <param name="add_extension" value="false"/>
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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parents: 0
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371 <param name="run_input_format" value="multiple_selection_list"/>
7
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372 <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
373 </conditional>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
374 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
375 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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376 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
377 <output name="experiments_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
378 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
379 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
380 <has_n_columns n="17"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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parents: 6
diff changeset
381 <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"
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parents: 6
diff changeset
382 <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"
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diff changeset
383 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
384 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
385 <output name="studies_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
386 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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387 <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
388 <has_n_columns n="7"/>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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parents: 6
diff changeset
389 <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
390 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
391 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
392 <output name="samples_table_out">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
393 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
394 <has_n_lines n="5"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
395 <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
396 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
397 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
398 <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
399 <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
400 <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
401 <has_n_columns n="8"/>
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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parents: 6
diff changeset
402 <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"
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parents: 6
diff changeset
403 <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
404 </assert_contents>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
405 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
406 </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
407 <!--Test 2: excel input of VIRAL samples with extended columns-->
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
408 <test>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
409 <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
410 <param name="action" value="add"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
411 <section name="test_submit_parameters">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
412 <param name="submit_dev" value="false" />
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
413 <param name="dry_run" value="true" />
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
414 </section>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
415 <conditional name="input_format_conditional">
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
416 <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"
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parents: 6
diff changeset
417 <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"
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parents: 1
diff changeset
418 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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parents: 1
diff changeset
419 <conditional name="run_input_format_conditional">
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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parents: 6
diff changeset
420 <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
421 <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"
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parents: 6
diff changeset
422 <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
423 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
424 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
425 </conditional>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
426 <param name="center" value="Some research center"/>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
427 <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
428 <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
429 <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
430 <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
431 <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
432 <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
433 </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
434 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
435 <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
436 <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
437 <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
438 <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
439 <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
440 <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
441 </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
442 </output>
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
443 <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
444 <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
445 <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
446 <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
447 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
448 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
449 <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
450 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
451 <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
452 <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
453 <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
454 <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
455 </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
456 </output>
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
465 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
466 </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
467 <!--Test 3: excel input of NON-VIRAL samples-->
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
468 <test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
469 <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
470 <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
471 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
472 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
473 <param name="dry_run" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
474 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
475 <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
476 <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
477 <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
478 <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
479 <conditional name="run_input_format_conditional">
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
480 <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
481 <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
482 <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
483 </conditional>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
484 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
485 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
486 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
487 <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
488 <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
489 <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
490 <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
491 <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
492 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
493 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
494 <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
495 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
496 <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
497 <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
498 <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
499 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
500 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
501 <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
502 <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
503 <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
504 <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
505 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
506 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
507 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
508 <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
509 <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
510 <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
511 <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
512 <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
513 <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
514 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
515 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
516 </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
517 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
518 <test expect_failure="true">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
519 <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
520 <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
521 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
522 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
523 <param name="dry_run" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
524 </section>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
525 <conditional name="input_format_conditional">
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
526 <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
527 <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
528 <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
529 <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
530 <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
531 <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
532 <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
533 <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
534 <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
535 <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
536 <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
537 <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
538 </collection>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
539 </element>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
540 </collection>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
541 </param>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
542 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
543 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
544 </conditional>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
545 <param name="center" value="Some research center"/>
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
546 <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
547 <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
548 <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
549 <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
550 </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
551 </test>
8
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
552 <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection + Idempotent submission -->
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
553 <test expect_failure="true">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
554 <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
555 <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
556 <section name="test_submit_parameters">
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
557 <param name="submit_dev" value="false" />
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
558 <param name="dry_run" value="false" />
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
559 </section>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
560 <param name="idempotent" value="true"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
561 <conditional name="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
562 <param name="add_extension" value="true"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
563 <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
564 <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
565 <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
566 <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
567 <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
568 <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
569 <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
570 <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
571 <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
572 <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
573 <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
574 </collection>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
575 </element>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
576 </collection>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
577 </param>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
578 </conditional>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
579 </conditional>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
580 </conditional>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
581 <param name="center" value="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
582 <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
583 <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
584 <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
585 <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
586 <has_text_matching expression="--auto_action"/>
d147d6455873 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents: 7
diff changeset
587 </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
588 </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
589 <!--Test 5: build tables from user input fields NON-VIRAL samples-->
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
590 <test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
591 <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
592 <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
593 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
594 <param name="submit_dev" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
595 <param name="dry_run" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
596 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
597 <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
598 <param name="input_format" value="build_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
599 <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
600 <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
601 <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
602 <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
603 <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
604 <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
605 <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
606 <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
607 <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
608 <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
609 <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
610 <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
611 <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
612 <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
613 <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
614 <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
615 <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
616 <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
617 <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
618 <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
619 <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
620 <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
621 <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
622 <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
623 <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
624 <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
625 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
626 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
627 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
628 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
629 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
630 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
631 </conditional>
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="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
633 <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
634 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
635 <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
636 <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
637 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
638 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
639 <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
640 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
641 <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
642 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
643 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
644 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
645 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
646 <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
647 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
648 <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
649 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
650 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
651 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
652 <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
653 <assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
654 <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
655 <has_n_columns n="8"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
656 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
657 </assert_contents>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
658 </output>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
659 </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
660 <!--Test 6: RUN failing build tables from user input fields NON-VIRAL samples-->
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
661 <test expect_failure="true">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
662 <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
663 <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
664 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
665 <param name="submit_dev" value="true" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
666 <param name="dry_run" value="false" />
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
667 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
668 <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
669 <param name="input_format" value="build_tables"/>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
670 <param name="add_extension" 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
671 <conditional name="conditional_viral_metadata">
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
672 <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
673 <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
674 <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
675 <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
676 <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
677 <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
678 <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
679 <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
680 <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
681 <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
682 <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
683 <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
684 <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
685 <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
686 <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
687 <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
688 <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
689 <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
690 <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
691 <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
692 <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
693 <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
694 <repeat name="rep_runs">
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
695 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
696 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
697 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
698 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
699 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
700 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
701 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
702 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
703 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
704 <assert_stdout>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
705 <has_text_matching expression="No ENA credentials defined"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
706 </assert_stdout>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
707 </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
708 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
709 also tests compression of uncompressed inputs and adding the .gz suffix -->
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
710 <test expect_failure="false">
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
711 <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
712 <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
713 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
714 <param name="submit_dev" value="true" />
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
715 <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
716 </section>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
717 <param name="test_submit" value="True"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
718 <conditional name="input_format_conditional">
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
719 <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
720 <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
721 <conditional name="conditional_viral_metadata">
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
722 <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
723 <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
724 <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
725 <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
726 <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
727 <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
728 <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
729 <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
730 <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
731 <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
732 <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
733 <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
734 <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
735 <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
736 <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
737 <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
738 <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
739 <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
740 <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
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
748 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
749 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
750 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
751 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
752 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
753 </conditional>
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="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
755 <assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
756 <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
757 <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
758 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
759 <not_has_text text="modify" />
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
760 </assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
761 </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
762 <!--Test 8: viral submission - User input metadata - Add extension = False-->
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
763 <test expect_failure="false">
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
764 <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
765 <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
766 <section name="test_submit_parameters">
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
767 <param name="submit_dev" value="false" />
7
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parents: 6
diff changeset
768 <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
769 </section>
0
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="test_submit" value="True"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
771 <conditional name="input_format_conditional">
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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parents: 6
diff changeset
772 <param name="add_extension" value="false"/>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
773 <param name="input_format" value="build_tables"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
774 <conditional name="conditional_viral_metadata">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
775 <param name="viral_sample" 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
776 <repeat name="rep_study">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
777 <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"
iuc
parents: 3
diff changeset
778 <param name="study_abstract" value="Test study abstract"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
779 <param name="study_type" value="Epigenetics"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
780 <param name="study_pubmed_id" value="Test study pubmedID"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
781 <repeat name="rep_sample">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
782 <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"
iuc
parents: 3
diff changeset
783 <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"
iuc
parents: 3
diff changeset
784 <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
785 <param name="tax_id" value="2697049"/>
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
786 <param name="collection_date" value="2020"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
787 <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"
iuc
parents: 3
diff changeset
788 <param name="host_common_name" value="Human"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
789 <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"
iuc
parents: 3
diff changeset
790 <param name="host_health_state" value="healthy"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
791 <param name="host_sex" value="female"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
792 <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"
iuc
parents: 3
diff changeset
793 <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"
iuc
parents: 3
diff changeset
794 <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"
iuc
parents: 3
diff changeset
795 <param name="isolate" value="sample_001"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
796 <repeat name="rep_experiment">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
797 <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"
iuc
parents: 3
diff changeset
798 <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"
iuc
parents: 3
diff changeset
799 <param name="library_strategy" value="CTS"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
800 <param name="library_source" value="GENOMIC"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
801 <param name="library_selection" value="PCR"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
802 <param name="library_layout" value="SINGLE"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
803 <param name="insert_size" value="150"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
804 <param name="library_construction_protocol" value="Test library construction"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
805 <param name="platform" value="ILLUMINA"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
806 <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"
iuc
parents: 3
diff changeset
807 <repeat name="rep_runs">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
808 <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
809 <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"
iuc
parents: 3
diff changeset
810 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
811 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
812 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
813 </repeat>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
814 </conditional>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
815 </conditional>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
816 </conditional>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
817 <param name="center" value="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
818 <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
819 <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"
iuc
parents: 3
diff changeset
820 <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"
iuc
parents: 3
diff changeset
821 <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
822 <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
823 </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
824 </test>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
825 <!--Test 9: modify option and auto compression - viral submission - User input metadata-->
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
826 <test expect_failure="false">
4
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
827 <conditional name="action_options">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
828 <param name="action" value="modify"/>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
829 <section name="test_submit_parameters">
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
830 <param name="submit_dev" value="false" />
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
831 <param name="dry_run" value="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
832 </section>
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents: 3
diff changeset
833 <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
834 <conditional name="input_format_conditional">
7
6f6537780379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents: 6
diff changeset
835 <param name="add_extension" value="fasle"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
836 <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
837 <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
838 <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
839 <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
840 <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
841 <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
842 <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
843 <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
844 <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
845 <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
846 <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
847 <param name="scientific_name" value="Test Sample scientific name"/>
7
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iuc
parents: 6
diff changeset
848 <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
849 <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
850 <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
851 <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
852 <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
853 <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
854 <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:
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855 <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"
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diff changeset
856 <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"
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diff changeset
857 <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"
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858 <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
859 <repeat name="rep_experiment">
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
860 <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"
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parents:
diff changeset
861 <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"
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parents:
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862 <param name="library_strategy" value="CTS"/>
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
863 <param name="library_source" value="GENOMIC"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
864 <param name="library_selection" value="PCR"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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865 <param name="library_layout" value="SINGLE"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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866 <param name="insert_size" value="150"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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867 <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"
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868 <param name="platform" value="ILLUMINA"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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869 <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:
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870 <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
871 <param name="run_base_name" value="run_from_hospital_X"/>
7
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iuc
parents: 6
diff changeset
872 <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/>
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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873 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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874 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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875 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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876 </repeat>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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877 </conditional>
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878 </conditional>
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879 </conditional>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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880 <param name="center" value="Some research center"/>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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parents:
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881 <assert_command>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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882 <has_text_matching expression="ena-upload-cli"/>
7
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parents: 6
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883 <has_text_matching expression="--data '1.fastqsanger.gz'"/>
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
884 <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"
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parents: 3
diff changeset
885 <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
886 <not_has_text text="add" />
0
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
887 </assert_command>
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
888 </test>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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889 </tests>
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diff changeset
890 <help><![CDATA[
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
891 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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892 The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
7
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893 It is also possible to submit an excel file by following the template in https://github.com/ELIXIR-Belgium/ENA-metadata-templates
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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894 ]]></help>
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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895 <citations>
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896 </citations>
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diff changeset
897 </tool>