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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@">0.5.3</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>
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9 <stdio>
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10 <regex match="Oops" source="stderr" level="fatal"/>
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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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19
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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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29
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30
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31 #if $action_options.input_format_conditional.input_format == "build_tables":
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32 cp $studies_table_path $studies_table_out &&
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33 cp $samples_table_path $samples_table_out &&
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34 cp $experiments_table_path $experiments_table_out &&
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35 cp $runs_table_path $runs_table_out &&
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36 #end if
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37 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
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38 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
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39 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
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40 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
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41 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
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42 #end if
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43 #if $action_options.input_format_conditional.input_format == "excel_tables":
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44 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
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45 #end if
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46 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
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47 webin_id=`grep 'username' $credentials`;
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48 if [ "\$webin_id" = "" ]; then
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49 ## No credentials in user defined preferences
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50 ## Fallback to global defined credentials (if exist)
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51 #import os
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52 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
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53 credentials_path=\${GALAXY_ENA_SECRETS};
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54 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
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55 if [ "\$webin_id" = "" ]; then
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56 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
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57 exit 1;
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58 fi;
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59 #else:
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60 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
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61 exit 1;
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62 #end if
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63 else
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64 credentials_path='$credentials';
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65 fi;
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66 #end if
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67
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68 #if $action_options.test_submit == "True" or $action_options.test_submit_parameters.dry_run == "true":
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69 credentials_path='test_fake_path';
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70 #if $action_options.test_submit_parameters.dry_run == "true" and $action_options.input_format_conditional.input_format == "excel_tables":
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71 echo "username: test_user" > \$credentials_path;
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72 echo "password: test_password" >> \$credentials_path;
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73 #end if
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74 #end if
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75
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76 ## create the list of files to upload and make the symlinks
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77 #import re
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78 #set $files_to_upload = list()
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79 #if $action_options.input_format_conditional.input_format == "build_tables":
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80 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
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81 #for $sample in $study.rep_sample:
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82 #for $experiment in $sample.rep_experiment:
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83 #for $run in $experiment.rep_runs:
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84 #for $file in $run.upload_files:
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85 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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86 #if $action_options.input_format_conditional.add_extension == "true":
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87 #set $extension = '.fastq'
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88 #else
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89 #set $extension = ''
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90 #end if
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91 #if $file.is_of_type('fastq', 'fastqsanger'):
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92 ## compression output is defined as safename_reads_file so no need to symlink
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93 #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
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94 gzip -c '$file' > $safename_reads_file &&
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95 #else:
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96 #if $action_options.input_format_conditional.add_extension == "true":
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97 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
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98 #set $compression = '.gz'
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99 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
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100 #set $compression = '.bz2'
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101 #end if
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102 #set $safename_reads_file = $safename_reads_file + $extension + $compression
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103 #end if
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104 ln -s '$file' $safename_reads_file &&
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105 #end if
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106 $files_to_upload.append(str($safename_reads_file))
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107 #end for
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108 #end for
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109 #end for
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110 #end for
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111 #end for
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112 #else:
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113 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list':
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114 #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection:
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115 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
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116 ## Always need to add .fastq + compression suffix because the name is based on the pair name which has no extensions
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117 #if $pair.forward.is_of_type('fastq', 'fastqsanger'):
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118 ## compress the file, no need to create the link then
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119 ## always add the compression suffix (.gz)
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120 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz'
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121 gzip -c '$file' > $safename_fwd_reads_file &&
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122 #else
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123 #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
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124 #set $compression = '.gz'
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125 #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
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126 #set $compression = '.bz2'
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127 #end if
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128 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression
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129 ln -s '$pair.forward' $safename_fwd_reads_file &&
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130 #end if
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131
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132 #if $pair.reverse.is_of_type('fastq', 'fastqsanger'):
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133 ## compress the file, no need to create the link then
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134 #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz'
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135 gzip -c '$file' > $safename_rev_reads_file &&
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136 #else
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137 #if $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
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138 #set $compression = '.bz2'
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139 #elif $pair.reverse.is_of_type('fastqsanger.gz', 'fastq.gz'):
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140 #set $compression = '.gz'
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141 #end if
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142 #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression
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143 ln -s '$pair.reverse' $safename_rev_reads_file &&
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144 #end if
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145 $files_to_upload.append(str($safename_fwd_reads_file))
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146 $files_to_upload.append(str($safename_rev_reads_file))
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147 #end for
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148 #end if
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149 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
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150 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
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151 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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152 #if $file.is_of_type('fastq', 'fastqsanger'):
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153 ## always compress add the gz extension
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154 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
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155 #set $safename_reads_file = $safename_reads_file + '.fastq.gz'
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156 #else
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157 #set $safename_reads_file = $safename_reads_file + '.gz'
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158 #end if
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159 gzip -c '$file' > $safename_reads_file &&
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160 #else
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161 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
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162 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
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163 #set $extension = '.fastq.gz'
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164 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
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165 #set $extension = '.fastq.bz2'
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166 #end if
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167 #set $safename_reads_file = $safename_reads_file + $extension
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168 #end if
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169 ln -s '$file' $safename_reads_file &&
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170 #end if
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171 $files_to_upload.append(str($safename_reads_file))
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172 #end for
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173 #end if
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174 #end if
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175
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176
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177 #if $action_options.test_submit_parameters.dry_run == "false" or $action_options.input_format_conditional.input_format == "excel_tables":
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178 #if $action_options.action == "add":
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179 ena-upload-cli
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180 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
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181 --action '$action_options.action'
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182 --center '$action_options.center'
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183 --secret \${credentials_path}
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184 --data
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185 #for $dataset in $files_to_upload:
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186 '$dataset'
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187 #end for
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188 #if $action_options.test_submit_parameters.dry_run == "true":
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189 --draft
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190 #end if
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191 #if $action_options.input_format_conditional.input_format != "excel_tables":
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192 --experiment '$experiments_table_path'
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193 --study '$studies_table_path'
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194 --run '$runs_table_path'
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195 --sample '$samples_table_path'
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196 #else
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197 --xlsx ./xlsx_input.xlsx
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198 #end if
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199 --action add
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200 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
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201 --checklist $action_options.input_format_conditional.checklist_id
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202 #else:
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203 #if $action_options.input_format_conditional.input_format == "build_tables":
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204 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
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205 --checklist ERC000033
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206 #end if
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207 #else:
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208 --checklist $action_options.input_format_conditional.checklist_id
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209 #end if
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210 #end if
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211
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212 #if $action_options.test_submit_parameters.submit_dev == "true":
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213 -d
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214 #end if
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215 >> '$output';
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216 #end if
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217
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218 #if $action_options.action == "modify":
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219 ena-upload-cli
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220 --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
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221 --action '$action_options.action'
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222 --center '$action_options.center'
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223 --secret \${credentials_path}
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224 --data
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225 #for $dataset in $files_to_upload:
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226 '$dataset'
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227 #end for
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228 #if $action_options.test_submit_parameters.dry_run == "true":
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229 --draft
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230 #end if
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231 #if $action_options.input_format_conditional.input_format != "excel_tables":
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232 --experiment '$experiments_table_path'
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233 --study '$studies_table_path'
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234 --run '$runs_table_path'
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235 --sample '$samples_table_path'
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236 #else
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237 --xlsx ./xlsx_input.xlsx
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238 --auto_action
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239 #end if
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240 --action 'modify'
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241 #if $action_options.input_format_conditional.input_format == "user_generated_tables":
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242 --checklist $action_options.input_format_conditional.checklist_id
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243 #else:
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244 #if $action_options.input_format_conditional.input_format == "build_tables":
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245 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
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246 --checklist ERC000033
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247 #end if
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248 #else:
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249 --checklist $action_options.input_format_conditional.checklist_id
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250 #end if
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251 #end if
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252 >> '$output';
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253 #end if
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254 #if $action_options.test_submit_parameters.dry_run == "false":
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255 echo -e 'center_name\t$action_options.center' >> '$output';
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256 echo -e 'action_option\t$action_options.action' >> '$output';
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257 #if $action_options.input_format_conditional.input_format == "build_tables":
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258 cp $studies_table_path_updated $studies_table_out 2>/dev/null;
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259 cp $samples_table_path_updated $samples_table_out 2>/dev/null;
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260 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
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261 cp $runs_table_path_updated $runs_table_out 2>/dev/null;
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262 #end if
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263 #else
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264 ## for the excel input case, copy the upload-cli generated tables to the output files
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265 ## this applies for both draft and real submissions
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266 cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
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267 cp './ENA_template_sample_updated.tsv' $samples_table_out;
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268 cp './ENA_template_study_updated.tsv' $studies_table_out;
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269 cp './ENA_template_run_updated.tsv' $runs_table_out;
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270 #end if
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271 #else:
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272 exit 0;
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273 #end if
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274
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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>
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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":
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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:
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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
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303 $runs.append((str($run.run_base_name),$run_files))
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304 #end for
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305
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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})
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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})
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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">
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329 <expand macro="test_submit_section"/>
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330 <param name="test_submit" type="hidden" value="False" />
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331 <expand macro="table_inputs_macro" />
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332 </when>
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333 <when value="modify">
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334 <expand macro="test_submit_section"/>
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335 <param name="test_submit" type="hidden" value="False" />
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336 <expand macro="table_inputs_macro" />
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337 </when>
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338 </conditional>
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339 </inputs>
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340 <outputs>
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341 <data name="output" format="txt" label="ENA submission receipt"/>
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342 <data name="studies_table_out" format="tabular" label="Studies table">
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343 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
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344 </data>
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345 <data name="samples_table_out" format="tabular" label="Samples table">
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346 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
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347 </data>
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348 <data name="experiments_table_out" format="tabular" label="Experiments table">
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349 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
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350 </data>
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351 <data name="runs_table_out" format="tabular" label="Runs table">
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352 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
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353 </data>
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354 </outputs>
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355 <tests>
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356 <!--Test 1: excel input of VIRAL samples -->
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357 <test>
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358 <conditional name="action_options">
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359 <param name="action" value="add"/>
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360 <section name="test_submit_parameters">
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361 <param name="submit_dev" value="false" />
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362 <param name="dry_run" value="true" />
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363 </section>
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364 <conditional name="input_format_conditional">
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365 <param name="input_format" value="excel_tables"/>
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366 <param name="checklist_id" value="ERC000033"/>
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367 <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
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368 <conditional name="run_input_format_conditional">
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369 <param name="add_extension" value="false"/>
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370 <param name="run_input_format" value="multiple_selection_list"/>
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371 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
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372 </conditional>
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373 </conditional>
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374 </conditional>
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375 <param name="center" value="Some research center"/>
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376 <output name="experiments_table_out">
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377 <assert_contents>
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378 <has_n_lines n="5"/>
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379 <has_n_columns n="17"/>
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380 <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"/>
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381 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
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382 </assert_contents>
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383 </output>
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384 <output name="studies_table_out">
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385 <assert_contents>
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386 <has_n_lines n="2"/>
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387 <has_n_columns n="7"/>
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388 <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(.*)"/>
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389 </assert_contents>
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390 </output>
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391 <output name="samples_table_out">
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392 <assert_contents>
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393 <has_n_lines n="5"/>
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394 <has_n_columns n="18"/>
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395 </assert_contents>
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396 </output>
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397 <output name="runs_table_out">
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398 <assert_contents>
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399 <has_n_lines n="5"/>
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400 <has_n_columns n="8"/>
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401 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
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402 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
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403 </assert_contents>
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404 </output>
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405 </test>
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406 <!--Test 2: excel input of VIRAL samples with extended columns-->
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407 <test>
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408 <conditional name="action_options">
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409 <param name="action" value="add"/>
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410 <section name="test_submit_parameters">
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411 <param name="submit_dev" value="false" />
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412 <param name="dry_run" value="true" />
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413 </section>
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414 <conditional name="input_format_conditional">
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415 <param name="input_format" value="excel_tables"/>
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416 <param name="checklist_id" value="ERC000033"/>
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417 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
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418 <conditional name="run_input_format_conditional">
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419 <param name="add_extension" value="false"/>
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420 <param name="run_input_format" value="multiple_selection_list"/>
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421 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
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422 </conditional>
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423 </conditional>
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424 </conditional>
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425 <param name="center" value="Some research center"/>
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426 <output name="experiments_table_out">
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427 <assert_contents>
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|
428 <has_n_lines n="5"/>
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429 <has_n_columns n="17"/>
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430 <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"/>
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|
431 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
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432 </assert_contents>
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433 </output>
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434 <output name="studies_table_out">
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435 <assert_contents>
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436 <has_n_lines n="2"/>
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437 <has_n_columns n="7"/>
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438 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/>
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439 <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(.*)"/>
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440 </assert_contents>
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441 </output>
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442 <output name="samples_table_out">
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443 <assert_contents>
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|
444 <has_n_lines n="5"/>
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445 <has_n_columns n="43"/>
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446 </assert_contents>
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447 </output>
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448 <output name="runs_table_out">
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449 <assert_contents>
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|
450 <has_n_lines n="5"/>
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451 <has_n_columns n="8"/>
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|
452 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
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|
453 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
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454 </assert_contents>
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455 </output>
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456 </test>
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457 <!--Test 3: excel input of NON-VIRAL samples-->
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458 <test>
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459 <conditional name="action_options">
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|
460 <param name="action" value="add"/>
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|
461 <section name="test_submit_parameters">
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|
462 <param name="submit_dev" value="false" />
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|
463 <param name="dry_run" value="true" />
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464 </section>
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|
465 <conditional name="input_format_conditional">
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|
466 <param name="input_format" value="excel_tables"/>
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|
467 <param name="checklist_id" value="ERC000011"/>
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|
468 <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/>
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|
469 <conditional name="run_input_format_conditional">
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|
470 <param name="add_extension" value="true"/>
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|
471 <param name="run_input_format" value="multiple_selection_list"/>
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|
472 <param name="data" value="sample_no_extension"/>
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|
473 </conditional>
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|
474 </conditional>
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|
475 </conditional>
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|
476 <param name="center" value="Some research center"/>
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|
|
477 <output name="experiments_table_out">
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|
478 <assert_contents>
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|
|
479 <has_n_lines n="2"/>
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|
|
480 <has_n_columns n="17"/>
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|
|
481 <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"/>
|
|
|
482 </assert_contents>
|
|
|
483 </output>
|
|
|
484 <output name="studies_table_out">
|
|
|
485 <assert_contents>
|
|
|
486 <has_n_lines n="2"/>
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|
|
487 <has_n_columns n="7"/>
|
|
|
488 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/>
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|
|
489 </assert_contents>
|
|
|
490 </output>
|
|
|
491 <output name="samples_table_out">
|
|
|
492 <assert_contents>
|
|
|
493 <has_n_lines n="2"/>
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|
|
494 <has_n_columns n="8"/>
|
|
|
495 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/>
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|
|
496 </assert_contents>
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|
|
497 </output>
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|
|
498 <output name="runs_table_out">
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|
|
499 <assert_contents>
|
|
|
500 <has_n_lines n="2"/>
|
|
|
501 <has_n_columns n="8"/>
|
|
|
502 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/>
|
|
|
503 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/>
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|
|
504 </assert_contents>
|
|
|
505 </output>
|
|
|
506 </test>
|
|
|
507 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
|
|
|
508 <test expect_failure="true">
|
|
|
509 <conditional name="action_options">
|
|
|
510 <param name="action" value="add"/>
|
|
|
511 <section name="test_submit_parameters">
|
|
|
512 <param name="submit_dev" value="false" />
|
|
|
513 <param name="dry_run" value="false" />
|
|
|
514 </section>
|
|
|
515 <conditional name="input_format_conditional">
|
|
|
516 <param name="add_extension" value="true"/>
|
|
|
517 <param name="input_format" value="excel_tables"/>
|
|
|
518 <param name="checklist_id" value="ERC000011"/>
|
|
|
519 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
|
|
|
520 <conditional name="run_input_format_conditional">
|
|
|
521 <param name="run_input_format" value="paired_list"/>
|
|
|
522 <param name="paired_end_collection">
|
|
|
523 <collection type="list:paired">
|
|
|
524 <element name="paired_run_name">
|
|
|
525 <collection type="paired">
|
|
|
526 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" />
|
|
|
527 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" />
|
|
|
528 </collection>
|
|
|
529 </element>
|
|
|
530 </collection>
|
|
|
531 </param>
|
|
|
532 </conditional>
|
|
|
533 </conditional>
|
|
|
534 </conditional>
|
|
|
535 <param name="center" value="Some research center"/>
|
|
|
536 <assert_command>
|
|
|
537 <has_text_matching expression="ena-upload-cli"/>
|
|
|
538 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
|
|
|
539 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
|
|
|
540 </assert_command>
|
|
|
541 </test>
|
|
|
542 <!--Test 5: build tables from user input fields NON-VIRAL samples-->
|
|
|
543 <test>
|
|
|
544 <conditional name="action_options">
|
|
|
545 <param name="action" value="add"/>
|
|
|
546 <section name="test_submit_parameters">
|
|
|
547 <param name="submit_dev" value="false" />
|
|
|
548 <param name="dry_run" value="true" />
|
|
|
549 </section>
|
|
|
550 <conditional name="input_format_conditional">
|
|
|
551 <param name="input_format" value="build_tables"/>
|
|
|
552 <param name="add_extension" value="true"/>
|
|
|
553 <conditional name="conditional_viral_metadata">
|
|
|
554 <param name="viral_sample" value="False"/>
|
|
|
555 <repeat name="rep_study">
|
|
|
556 <param name="study_title" value="Test study title"/>
|
|
|
557 <param name="study_abstract" value="Test study abstract"/>
|
|
|
558 <param name="study_type" value="Epigenetics"/>
|
|
|
559 <param name="study_pubmed_id" value="Test study pubmedID"/>
|
|
|
560 <repeat name="rep_sample">
|
|
|
561 <param name="sample_title" value="Test Sample title"/>
|
|
|
562 <param name="sample_description" value="Test Sample description"/>
|
|
|
563 <param name="scientific_name" value="Test Sample scientific name"/>
|
|
|
564 <param name="tax_id" value="Test Sample tax_id"/>
|
|
|
565 <repeat name="rep_experiment">
|
|
|
566 <param name="experiment_title" value="Test experiment title"/>
|
|
|
567 <param name="experiment_design" value="Test experiment design description"/>
|
|
|
568 <param name="library_strategy" value="CTS"/>
|
|
|
569 <param name="library_source" value="GENOMIC"/>
|
|
|
570 <param name="library_selection" value="PCR"/>
|
|
|
571 <param name="library_layout" value="SINGLE"/>
|
|
|
572 <param name="insert_size" value="150"/>
|
|
|
573 <param name="library_construction_protocol" value="Test library construction"/>
|
|
|
574 <param name="platform" value="ILLUMINA"/>
|
|
|
575 <param name="instrument_model" value="Illumina HiSeq 4000"/>
|
|
|
576 <repeat name="rep_runs">
|
|
|
577 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
|
|
|
578 </repeat>
|
|
|
579 </repeat>
|
|
|
580 </repeat>
|
|
|
581 </repeat>
|
|
|
582 </conditional>
|
|
|
583 </conditional>
|
|
|
584 </conditional>
|
|
|
585 <param name="center" value="Some research center"/>
|
|
|
586 <output name="experiments_table_out">
|
|
|
587 <assert_contents>
|
|
|
588 <has_n_lines n="2"/>
|
|
|
589 <has_n_columns n="17"/>
|
|
|
590 </assert_contents>
|
|
|
591 </output>
|
|
|
592 <output name="studies_table_out">
|
|
|
593 <assert_contents>
|
|
|
594 <has_n_lines n="2"/>
|
|
|
595 <has_n_columns n="8"/>
|
|
|
596 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
|
|
|
597 </assert_contents>
|
|
|
598 </output>
|
|
|
599 <output name="samples_table_out">
|
|
|
600 <assert_contents>
|
|
|
601 <has_n_lines n="2"/>
|
|
|
602 <has_n_columns n="8"/>
|
|
|
603 </assert_contents>
|
|
|
604 </output>
|
|
|
605 <output name="runs_table_out">
|
|
|
606 <assert_contents>
|
|
|
607 <has_n_lines n="3"/>
|
|
|
608 <has_n_columns n="8"/>
|
|
|
609 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
|
|
|
610 </assert_contents>
|
|
|
611 </output>
|
|
|
612 </test>
|
|
|
613 <!--Test 6: RUN failing build tables from user input fields NON-VIRAL samples-->
|
|
|
614 <test expect_failure="true">
|
|
|
615 <conditional name="action_options">
|
|
|
616 <param name="action" value="add"/>
|
|
|
617 <section name="test_submit_parameters">
|
|
|
618 <param name="submit_dev" value="true" />
|
|
|
619 <param name="dry_run" value="false" />
|
|
|
620 </section>
|
|
|
621 <conditional name="input_format_conditional">
|
|
|
622 <param name="input_format" value="build_tables"/>
|
|
|
623 <param name="add_extension" value="true"/>
|
|
|
624 <conditional name="conditional_viral_metadata">
|
|
|
625 <param name="viral_sample" value="false"/>
|
|
|
626 <repeat name="rep_study">
|
|
|
627 <param name="study_title" value="Test study title"/>
|
|
|
628 <param name="study_abstract" value="Test study abstract"/>
|
|
|
629 <param name="study_type" value="Epigenetics"/>
|
|
|
630 <param name="study_pubmed_id" value="Test study pubmedID"/>
|
|
|
631 <repeat name="rep_sample">
|
|
|
632 <param name="sample_title" value="Test Sample title"/>
|
|
|
633 <param name="sample_description" value="Test Sample description"/>
|
|
|
634 <param name="scientific_name" value="Test Sample scientific name"/>
|
|
|
635 <param name="tax_id" value="Test Sample tax_id"/>
|
|
|
636 <repeat name="rep_experiment">
|
|
|
637 <param name="experiment_title" value="Test experiment title"/>
|
|
|
638 <param name="experiment_design" value="Test experiment design description"/>
|
|
|
639 <param name="library_strategy" value="CTS"/>
|
|
|
640 <param name="library_source" value="GENOMIC"/>
|
|
|
641 <param name="library_selection" value="PCR"/>
|
|
|
642 <param name="library_layout" value="SINGLE"/>
|
|
|
643 <param name="insert_size" value="150"/>
|
|
|
644 <param name="library_construction_protocol" value="Test library construction"/>
|
|
|
645 <param name="platform" value="ILLUMINA"/>
|
|
|
646 <param name="instrument_model" value="Illumina HiSeq 4000"/>
|
|
|
647 <repeat name="rep_runs">
|
|
|
648 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
|
|
|
649 </repeat>
|
|
|
650 </repeat>
|
|
|
651 </repeat>
|
|
|
652 </repeat>
|
|
|
653 </conditional>
|
|
|
654 </conditional>
|
|
|
655 </conditional>
|
|
|
656 <param name="center" value="Some research center"/>
|
|
|
657 <assert_stdout>
|
|
|
658 <has_text_matching expression="No ENA credentials defined"/>
|
|
|
659 </assert_stdout>
|
|
|
660 </test>
|
|
|
661 <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
|
|
|
662 also tests compression of uncompressed inputs and adding the .gz suffix -->
|
|
|
663 <test expect_failure="true">
|
|
|
664 <conditional name="action_options">
|
|
|
665 <param name="action" value="add"/>
|
|
|
666 <section name="test_submit_parameters">
|
|
|
667 <param name="submit_dev" value="true" />
|
|
|
668 <param name="dry_run" value="false" />
|
|
|
669 </section>
|
|
|
670 <param name="test_submit" value="True"/>
|
|
|
671 <conditional name="input_format_conditional">
|
|
|
672 <param name="add_extension" value="true"/>
|
|
|
673 <param name="input_format" value="build_tables"/>
|
|
|
674 <conditional name="conditional_viral_metadata">
|
|
|
675 <param name="viral_sample" value="false"/>
|
|
|
676 <repeat name="rep_study">
|
|
|
677 <param name="study_title" value="Test study title"/>
|
|
|
678 <param name="study_abstract" value="Test study abstract"/>
|
|
|
679 <param name="study_type" value="Epigenetics"/>
|
|
|
680 <param name="study_pubmed_id" value="Test study pubmedID"/>
|
|
|
681 <repeat name="rep_sample">
|
|
|
682 <param name="sample_title" value="Test Sample title"/>
|
|
|
683 <param name="sample_description" value="Test Sample description"/>
|
|
|
684 <param name="scientific_name" value="Test Sample scientific name"/>
|
|
|
685 <param name="tax_id" value="Test Sample tax_id"/>
|
|
|
686 <repeat name="rep_experiment">
|
|
|
687 <param name="experiment_title" value="Test experiment title"/>
|
|
|
688 <param name="experiment_design" value="Test experiment design description"/>
|
|
|
689 <param name="library_strategy" value="CTS"/>
|
|
|
690 <param name="library_source" value="GENOMIC"/>
|
|
|
691 <param name="library_selection" value="PCR"/>
|
|
|
692 <param name="library_layout" value="SINGLE"/>
|
|
|
693 <param name="insert_size" value="150"/>
|
|
|
694 <param name="library_construction_protocol" value="Test library construction"/>
|
|
|
695 <param name="platform" value="ILLUMINA"/>
|
|
|
696 <param name="instrument_model" value="Illumina HiSeq 4000"/>
|
|
|
697 <repeat name="rep_runs">
|
|
|
698 <param name="run_base_name" value="run_from_hospital_X"/>
|
|
|
699 <param name="upload_files" value="sample.fq,sample.fq" ftype="fastqsanger"/>
|
|
|
700 </repeat>
|
|
|
701 </repeat>
|
|
|
702 </repeat>
|
|
|
703 </repeat>
|
|
|
704 </conditional>
|
|
|
705 </conditional>
|
|
|
706 </conditional>
|
|
|
707 <param name="center" value="Some research center"/>
|
|
|
708 <assert_command>
|
|
|
709 <has_text_matching expression="ena-upload-cli"/>
|
|
|
710 <has_text_matching expression="--data 'sample.fq.fastq.gz' 'sample.fq.fastq.gz'"/>
|
|
|
711 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
|
|
|
712 <not_has_text text="modify" />
|
|
|
713 </assert_command>
|
|
|
714 <assert_stderr>
|
|
|
715 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
|
|
|
716 </assert_stderr>
|
|
|
717 </test>
|
|
|
718 <!--Test 8: viral submission - User input metadata - Add extension = False-->
|
|
|
719 <test expect_failure="true">
|
|
|
720 <conditional name="action_options">
|
|
|
721 <param name="action" value="add"/>
|
|
|
722 <section name="test_submit_parameters">
|
|
|
723 <param name="submit_dev" value="false" />
|
|
|
724 <param name="dry_run" value="false" />
|
|
|
725 </section>
|
|
|
726 <param name="test_submit" value="True"/>
|
|
|
727 <conditional name="input_format_conditional">
|
|
|
728 <param name="add_extension" value="False"/>
|
|
|
729 <param name="input_format" value="build_tables"/>
|
|
|
730 <conditional name="conditional_viral_metadata">
|
|
|
731 <param name="viral_sample" value="true"/>
|
|
|
732 <repeat name="rep_study">
|
|
|
733 <param name="study_title" value="Test study title"/>
|
|
|
734 <param name="study_abstract" value="Test study abstract"/>
|
|
|
735 <param name="study_type" value="Epigenetics"/>
|
|
|
736 <param name="study_pubmed_id" value="Test study pubmedID"/>
|
|
|
737 <repeat name="rep_sample">
|
|
|
738 <param name="sample_title" value="Test Sample title"/>
|
|
|
739 <param name="sample_description" value="Test Sample description"/>
|
|
|
740 <param name="scientific_name" value="Test Sample scientific name"/>
|
|
|
741 <param name="tax_id" value="Test Sample tax_id"/>
|
|
|
742 <param name="collection_date" value="2020"/>
|
|
|
743 <param name="geo_location_country" value="Belgium"/>
|
|
|
744 <param name="host_common_name" value="Human"/>
|
|
|
745 <param name="host_subject_id" value="Patient_001"/>
|
|
|
746 <param name="host_health_state" value="healthy"/>
|
|
|
747 <param name="host_sex" value="female"/>
|
|
|
748 <param name="host_scientific_name" value="homo sapiens"/>
|
|
|
749 <param name="collector_name" value="John The Collector"/>
|
|
|
750 <param name="collecting_institution" value="Hospital 01"/>
|
|
|
751 <param name="isolate" value="sample_001"/>
|
|
|
752 <repeat name="rep_experiment">
|
|
|
753 <param name="experiment_title" value="Test experiment title"/>
|
|
|
754 <param name="experiment_design" value="Test experiment design description"/>
|
|
|
755 <param name="library_strategy" value="CTS"/>
|
|
|
756 <param name="library_source" value="GENOMIC"/>
|
|
|
757 <param name="library_selection" value="PCR"/>
|
|
|
758 <param name="library_layout" value="SINGLE"/>
|
|
|
759 <param name="insert_size" value="150"/>
|
|
|
760 <param name="library_construction_protocol" value="Test library construction"/>
|
|
|
761 <param name="platform" value="ILLUMINA"/>
|
|
|
762 <param name="instrument_model" value="Illumina HiSeq 4000"/>
|
|
|
763 <repeat name="rep_runs">
|
|
|
764 <param name="run_base_name" value="run_from_hospital_X"/>
|
|
|
765 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
|
|
|
766 </repeat>
|
|
|
767 </repeat>
|
|
|
768 </repeat>
|
|
|
769 </repeat>
|
|
|
770 </conditional>
|
|
|
771 </conditional>
|
|
|
772 </conditional>
|
|
|
773 <param name="center" value="Some research center"/>
|
|
|
774 <assert_command>
|
|
|
775 <has_text_matching expression="ena-upload-cli"/>
|
|
|
776 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
|
|
|
777 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
|
|
|
778 <has_text_matching expression="--checklist ERC000033"/>
|
|
|
779 </assert_command>
|
|
|
780 <assert_stderr>
|
|
|
781 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
|
|
|
782 </assert_stderr>
|
|
|
783 </test>
|
|
|
784 <!--Test 9: modify option and auto compression - viral submission - User input metadata-->
|
|
|
785 <test expect_failure="true">
|
|
|
786 <conditional name="action_options">
|
|
|
787 <param name="action" value="modify"/>
|
|
|
788 <section name="test_submit_parameters">
|
|
|
789 <param name="submit_dev" value="false" />
|
|
|
790 <param name="dry_run" value="false" />
|
|
|
791 </section>
|
|
|
792 <param name="test_submit" value="True"/>
|
|
|
793 <conditional name="input_format_conditional">
|
|
|
794 <param name="add_extension" value="False"/>
|
|
|
795 <param name="input_format" value="build_tables"/>
|
|
|
796 <conditional name="conditional_viral_metadata">
|
|
|
797 <param name="viral_sample" value="True"/>
|
|
|
798 <repeat name="rep_study">
|
|
|
799 <param name="study_title" value="Test study title"/>
|
|
|
800 <param name="study_abstract" value="Test study abstract"/>
|
|
|
801 <param name="study_type" value="Epigenetics"/>
|
|
|
802 <param name="study_pubmed_id" value="Test study pubmedID"/>
|
|
|
803 <repeat name="rep_sample">
|
|
|
804 <param name="sample_title" value="Test Sample title"/>
|
|
|
805 <param name="sample_description" value="Test Sample description"/>
|
|
|
806 <param name="scientific_name" value="Test Sample scientific name"/>
|
|
|
807 <param name="tax_id" value="Test Sample tax_id"/>
|
|
|
808 <param name="collection_date" value="2020"/>
|
|
|
809 <param name="geo_location_country" value="Belgium"/>
|
|
|
810 <param name="host_common_name" value="Human"/>
|
|
|
811 <param name="host_subject_id" value="Patient_001"/>
|
|
|
812 <param name="host_health_state" value="healthy"/>
|
|
|
813 <param name="host_sex" value="female"/>
|
|
|
814 <param name="host_scientific_name" value="homo sapiens"/>
|
|
|
815 <param name="collector_name" value="John The Collector"/>
|
|
|
816 <param name="collecting_institution" value="Hospital 01"/>
|
|
|
817 <param name="isolate" value="sample_001"/>
|
|
|
818 <repeat name="rep_experiment">
|
|
|
819 <param name="experiment_title" value="Test experiment title"/>
|
|
|
820 <param name="experiment_design" value="Test experiment design description"/>
|
|
|
821 <param name="library_strategy" value="CTS"/>
|
|
|
822 <param name="library_source" value="GENOMIC"/>
|
|
|
823 <param name="library_selection" value="PCR"/>
|
|
|
824 <param name="library_layout" value="SINGLE"/>
|
|
|
825 <param name="insert_size" value="150"/>
|
|
|
826 <param name="library_construction_protocol" value="Test library construction"/>
|
|
|
827 <param name="platform" value="ILLUMINA"/>
|
|
|
828 <param name="instrument_model" value="Illumina HiSeq 4000"/>
|
|
|
829 <repeat name="rep_runs">
|
|
|
830 <param name="run_base_name" value="run_from_hospital_X"/>
|
|
|
831 <param name="upload_files" value="sample.fq" ftype="fastqsanger"/>
|
|
|
832 </repeat>
|
|
|
833 </repeat>
|
|
|
834 </repeat>
|
|
|
835 </repeat>
|
|
|
836 </conditional>
|
|
|
837 </conditional>
|
|
|
838 </conditional>
|
|
|
839 <param name="center" value="Some research center"/>
|
|
|
840 <assert_command>
|
|
|
841 <has_text_matching expression="ena-upload-cli"/>
|
|
|
842 <has_text_matching expression="--data 'sample.fq.gz'"/>
|
|
|
843 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
|
|
|
844 <has_text_matching expression="--checklist ERC000033"/>
|
|
|
845 <not_has_text text="add" />
|
|
|
846 </assert_command>
|
|
|
847 <assert_stderr>
|
|
|
848 <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
|
|
|
849 </assert_stderr>
|
|
|
850 </test>
|
|
|
851 </tests>
|
|
|
852 <help><![CDATA[
|
|
|
853 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
|
|
|
854 The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
|
|
|
855 It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing
|
|
|
856 For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing
|
|
|
857 ]]></help>
|
|
|
858 <citations>
|
|
|
859 </citations>
|
|
|
860 </tool>
|
