| Next changeset 1:57251c760cab (2021-04-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a" |
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added:
README.md ena_upload.xml extract_tables.py process_xlsx.py samples_macros.xml test-data/1.fastqsanger.gz test-data/metadata_test_nonviral.xlsx test-data/metadata_test_viral.xlsx test-data/sample.fq tool-data/geographic_location_1.loc.sample tool-data/host_health_state_1.loc.sample tool-data/host_sex_1.loc.sample tool-data/instrument_model.loc.sample tool-data/library_layout.loc.sample tool-data/library_selection.loc.sample tool-data/library_source.loc.sample tool-data/library_strategy.loc.sample tool-data/study_type.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 382518f24d6d README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Nov 28 09:45:44 2020 +0000 |
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| @@ -0,0 +1,31 @@ +# ena-upload-wrapper +Galaxy wrapper for ena-cli-upload + +This tool is shipped in a ready to use Galaxy container found [here](https://github.com/ELIXIR-Belgium/ena-upload-container). + +## Setting up credentials on Galaxy + +The admin of the server can set up global credentials through a file with the format: +``` +username: webin_id +password: webin_password +``` + +The path to this file must be exported as an environment variable called $GALAXY_ENA_SECRETS + +Alternatively, the admin can enable users to set their own credentials for this tool. +To enable it, make sure the file `config/user_preferences_extra_conf.yml` has the following section: + +``` + ena_webin_account: + description: Your ENA Webin account details + inputs: + - name: webin_id + label: ENA Webin ID + type: text + required: False + - name: password + label: Password + type: password + required: False +``` |
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| diff -r 000000000000 -r 382518f24d6d ena_upload.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ena_upload.xml Sat Nov 28 09:45:44 2020 +0000 |
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| b'@@ -0,0 +1,549 @@\n+<tool id="ena_upload" name="ENA Upload tool" version="0.3" profile="20.01" license="MIT">\n+ <macros>\n+ <token name="@VERSION@">0.2.4</token>\n+ <import>samples_macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>\n+ <requirement type="package" version="1.2.0">xlrd</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+mkdir ./submission_files; \n+\n+#set working_dir = os.getcwd()\n+#set $dry_run_option = "False"\n+#set viral_submission = "False"\n+#if $action_options.input_format_conditional.input_format == "build_tables":\n+ python \'$__tool_directory__/extract_tables.py\' --action $action_options.action --out_dir ./submission_files --studies $studies_json;\n+ #set $studies_table_path = \'./submission_files/studies.tsv\'\n+ #set $samples_table_path = \'./submission_files/samples.tsv\'\n+ #set $experiments_table_path = \'./submission_files/experiments.tsv\'\n+ #set $runs_table_path = \'./submission_files/runs.tsv\'\n+#end if\n+\n+#if $action_options.input_format_conditional.input_format == "excel_tables":\n+ python \'$__tool_directory__/process_xlsx.py\'\n+ #if $action_options.input_format_conditional.viral_submission == "true":\n+ --vir \n+ #end if\n+ --action \'$action_options.action\' --form \'$action_options.input_format_conditional.xlsx_file\' --out_dir ./submission_files ;\n+ #set $studies_table_path = \'./submission_files/studies.tsv\'\n+ #set $samples_table_path = \'./submission_files/samples.tsv\'\n+ #set $experiments_table_path = \'./submission_files/experiments.tsv\'\n+ #set $runs_table_path = \'./submission_files/runs.tsv\'\n+ #if $action_options.input_format_conditional.dry_run == "true":\n+ #set $dry_run_option = "True"\n+ #end if\n+#end if\n+\n+#if $action_options.input_format_conditional.input_format != "user_generated_tables":\n+ cp $studies_table_path $studies_table_out;\n+ cp $samples_table_path $samples_table_out;\n+ cp $experiments_table_path $experiments_table_out;\n+ cp $runs_table_path $runs_table_out;\n+ #if $action_options.input_format_conditional.dry_run == "true":\n+ #set $dry_run_option = "True"\n+ #end if\n+#end if\n+\n+\n+#if $dry_run_option == "False" and $action_options.test_submit == "False":\n+ webin_id=`grep \'username\' $credentials`;\n+ if [ "\\$webin_id" = "" ]; then\n+ ## No credentials in user defined preferences \n+ ## Fallback to global defined credentials (if exist) \n+ #import os\n+ #if os.path.isfile(os.environ.get(\'GALAXY_ENA_SECRETS\', \'\')):\n+ credentials_path=\\${ENA_SECRETS}; \n+ webin_id=`grep \'username\' \\$GALAXY_ENA_SECRETS`;\n+ if [ "\\$webin_id" = "" ]; then\n+ echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";\n+ exit 1;\n+ fi;\n+ #else:\n+ echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";\n+ exit 1;\n+ #end if\n+ else\n+ credentials_path=\'$credentials\';\n+ fi;\n+#end if\n+\n+#if $action_options.test_submit == "True":\n+ credentials_path=\'test_fake_path\';\n+#end if\n+\n+## create the list of files to upload and make the symlinks \n+#import re \n+#set $files_to_upload = list()\n+#if $action_options.input_format_conditional.input_format == "build_tables":\n+ #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:\n+ #for $sample in $study.rep_sample:\n+ #for $experiment in $sample.rep_experiment:\n+ #for $run in $experiment.rep_runs:\n+ #for $file in $run.upload_files:\n+ #set $safename_reads_file = re.sub(\'[^\\w\\-_\\.]\', \'_\', $file.element_identifier)\n+ ln -s \'$file\' $safename_reads_file &&\n+ $files_to_upload.append(str($safename_reads_file))'..b'repeat name="rep_sample">\n+ <param name="sample_title" value="Test Sample title"/>\n+ <param name="sample_description" value="Test Sample description"/>\n+ <param name="scientific_name" value="Test Sample scientific name"/>\n+ <param name="tax_id" value="Test Sample tax_id"/>\n+ <param name="collection_date" value="2020"/>\n+ <param name="geo_location_country" value="Belgium"/>\n+ <param name="host_common_name" value="Human"/>\n+ <param name="host_subject_id" value="Patient_001"/>\n+ <param name="host_health_state" value="healthy"/>\n+ <param name="host_sex" value="female"/>\n+ <param name="host_scientific_name" value="homo sapiens"/>\n+ <param name="collector_name" value="John The Collector"/>\n+ <param name="collecting_institution" value="Hospital 01"/>\n+ <param name="isolate" value="sample_001"/>\n+ <repeat name="rep_experiment">\n+ <param name="experiment_title" value="Test experiment title"/>\n+ <param name="experiment_design" value="Test experiment design description"/>\n+ <param name="library_strategy" value="CTS"/>\n+ <param name="library_source" value="GENOMIC"/>\n+ <param name="library_selection" value="PCR"/>\n+ <param name="library_layout" value="SINGLE"/>\n+ <param name="insert_size" value="150"/>\n+ <param name="library_construction_protocol" value="Test library construction"/>\n+ <param name="platform" value="ILLUMINA"/>\n+ <param name="instrument_model" value="Illumina HiSeq 4000"/>\n+ <repeat name="rep_runs">\n+ <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>\n+ </repeat>\n+ </repeat>\n+ </repeat>\n+ </repeat>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <param name="center" value="Some research center"/>\n+ <assert_command>\n+ <has_text_matching expression="ena-upload-cli"/>\n+ <has_text_matching expression="--data \'1.fastqsanger.gz\' \'sample.fq\'"/>\n+ <has_text_matching expression="--action \'add\' --center \'Some research center\'"/>\n+ <has_text_matching expression="--vir"/>\n+ </assert_command>\n+ <assert_stderr>\n+ <has_text_matching expression="ENA_upload: error: Oops, the file test_fake_path does not exist"/>\n+ </assert_stderr>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli\n+ 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\n+ 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\n+ For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1U4VdcczsIecIXxseV8svE1zO_CBUadog/view?usp=sharing \n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 382518f24d6d extract_tables.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_tables.py Sat Nov 28 09:45:44 2020 +0000 |
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| @@ -0,0 +1,93 @@ +import argparse +import json +import pathlib +from datetime import datetime + +FILE_FORMAT = 'fastq' + +parser = argparse.ArgumentParser() +parser.add_argument('--studies', dest='studies_json_path', required=True) +parser.add_argument('--out_dir', dest='out_path', required=True) +parser.add_argument('--action', dest='action', required=True) +args = parser.parse_args() + +with open(args.studies_json_path, 'r') as studies_json_file: + studies_dict = json.load(studies_json_file) +studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w') +studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type', + 'study_abstract', 'pubmed_id', 'submission_date']) + '\n') +samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w') +experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w') +experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias', + 'sample_alias', 'design_description', 'library_name', + 'library_strategy', 'library_source', 'library_selection', + 'library_layout', 'insert_size', + 'library_construction_protocol', 'platform', 'instrument_model', + 'submission_date']) + '\n') +runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w') +runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name', + 'file_format', 'file_checksum', 'submission_date']) + '\n') + +action = args.action + +dt_oobj = datetime.now(tz=None) +timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S") +for study_index, study in enumerate(studies_dict): + study_alias = 'study_' + str(study_index) + '_' + timestamp + studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'], + study['type'], study['abstract'], study['pubmed_id'], + 'ENA_submission_data'])) + if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample + samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name', + 'taxon_id', 'sample_description', 'collection_date', + 'geographic_location', 'host_common_name', 'host_subject_id', + 'host_health_state', 'host_sex', 'host_scientific_name', + 'collector_name', 'collecting_institution', 'isolate', + 'submission_date']) + '\n') + else: + samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name', + 'taxon_id', 'sample_description', 'submission_date']) + '\n') + for sample_index, sample in enumerate(study['samples']): + sample_alias = 'sample_' + str(sample_index) + '_' + timestamp + if "geo_location" in sample.keys(): # sample belongs to a viral sample + if sample['collector_name'] == '': + sample['collector_name'] = 'unknown' + samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'], + sample['tax_name'], sample['tax_id'], + sample['description'], sample['collection_date'], + sample['geo_location'], sample['host_common_name'], + sample['host_subject_id'], sample['host_health_state'], + sample['host_sex'], sample['host_scientific_name'], + sample['collector_name'], + sample['collecting_institution'], sample['isolate'], + 'ENA_submission_date']) + '\n') + else: + samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'], + sample['tax_name'], sample['tax_id'], + sample['description'], 'ENA_submission_date']) + '\n') + for exp_index, exp in enumerate(sample['experiments']): + exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp + lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index) + experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'], + study_alias, sample_alias, exp['experiment_design'], + lib_alias, exp['library_strategy'], + exp['library_source'], exp['library_selection'], + exp['library_layout'].lower(), exp['insert_size'], + exp['library_construction_protocol'], + exp['platform'], exp['instrument_model'], + 'submission_date_ENA']) + '\n') + run_index = 0 + # exp['runs'] is a list of lists + for run in exp['runs']: + run_index += 1 + run_alias = '.'.join(['run_' + str(run_index), str(exp_index), str(sample_index)]) \ + + '_' + timestamp + for file_entry in run: + runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias, + file_entry, FILE_FORMAT, 'file_checksum', + 'submission_date_ENA']) + '\n') + +studies_table.close() +samples_table.close() +experiments_table.close() +runs_table.close() |
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| diff -r 000000000000 -r 382518f24d6d process_xlsx.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_xlsx.py Sat Nov 28 09:45:44 2020 +0000 |
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| b'@@ -0,0 +1,173 @@\n+import argparse\n+import pathlib\n+import sys\n+\n+import xlrd\n+\n+\n+FILE_FORMAT = \'fastq\'\n+\n+\n+def extract_data(xl_sheet, expected_columns):\n+ """\n+ 1. Check that the columns I expect are present in the sheet\n+ (any order and mixed with others, it\'s just a verification that\n+ the user filled the correct template)\n+ 2. Fill a dictionary with the rows data indexed by first column in list"""\n+ sheet_columns = {}\n+ for sh_col in range(xl_sheet.ncols):\n+ if xl_sheet.cell(0, sh_col).value in expected_columns:\n+ if xl_sheet.cell(0, sh_col).value in sheet_columns.keys():\n+ sys.exit("Duplicated columns")\n+ else:\n+ sheet_columns[xl_sheet.cell(0, sh_col).value] = sh_col\n+ for col in range(len(expected_columns)):\n+ assert expected_columns[col] in sheet_columns.keys(), \\\n+ "Expected column %s not found" % expected_columns[col]\n+\n+ # fetch rows in a dict\n+ data_dict = {}\n+ # the first of the expected columns will be the index\n+ index_col = sheet_columns[expected_columns[0]]\n+ # skip first 2 rows: column names + comments rows\n+ for row_id in range(2, xl_sheet.nrows):\n+ row_dict = {}\n+ for col in range(1, len(expected_columns)):\n+ sheet_col_index = sheet_columns[expected_columns[col]]\n+ row_dict[expected_columns[col]] = xl_sheet.cell(row_id, sheet_col_index).value\n+ # should check for duplicate alias/ids?\n+ data_dict[xl_sheet.cell(row_id, index_col).value] = row_dict\n+ return data_dict\n+\n+\n+parser = argparse.ArgumentParser()\n+parser.add_argument(\'--form\', dest=\'xlsx_path\', required=True)\n+parser.add_argument(\'--out_dir\', dest=\'out_path\', required=True)\n+parser.add_argument(\'--action\', dest=\'action\', required=True)\n+parser.add_argument(\'--vir\', dest=\'viral_submission\', required=False, action=\'store_true\')\n+args = parser.parse_args()\n+\n+xl_workbook = xlrd.open_workbook(args.xlsx_path)\n+\n+# PARSE STUDIES\n+#################\n+xl_sheet = xl_workbook.sheet_by_name(\'ENA_study\')\n+if xl_sheet.nrows < 3:\n+ raise ValueError(\'No entries found in studies sheet\')\n+studies_dict = {}\n+studies_col = [\'alias\', \'title\', \'study_type\', \'study_abstract\']\n+studies_dict = extract_data(xl_sheet, studies_col)\n+\n+# PARSE SAMPLES\n+#################\n+xl_sheet = xl_workbook.sheet_by_name(\'ENA_sample\')\n+if xl_sheet.nrows < 3:\n+ raise ValueError(\'No entries found in samples\')\n+if args.viral_submission:\n+ samples_cols = [\'alias\', \'title\', \'scientific_name\', \'sample_description\',\n+ \'geographic location (country and/or sea)\', \'host common name\',\n+ \'host health state\', \'host sex\', \'host scientific name\', \'collector name\',\n+ \'collection date\', \'collecting institution\', \'isolate\']\n+else:\n+ samples_cols = [\'alias\', \'title\', \'scientific_name\', \'sample_description\']\n+samples_dict = extract_data(xl_sheet, samples_cols)\n+\n+# PARSE EXPERIMENTS\n+#################\n+xl_sheet = xl_workbook.sheet_by_name(\'ENA_experiment\')\n+if xl_sheet.nrows < 3:\n+ raise ValueError(\'No experiments found in experiments sheet\')\n+exp_columns = [\'alias\', \'title\', \'study_alias\', \'sample_alias\', \'design_description\', \'library_name\',\n+ \'library_strategy\', \'library_source\', \'library_selection\', \'library_layout\',\n+ \'insert_size\', \'library_construction_protocol\', \'platform\', \'instrument_model\']\n+experiments_dict = extract_data(xl_sheet, exp_columns)\n+\n+# PARSE RUNS SHEET\n+#################\n+xl_sheet = xl_workbook.sheet_by_name(\'ENA_run\')\n+if xl_sheet.nrows < 3:\n+ raise ValueError(\'No entries found in runs sheet\')\n+run_cols = [\'alias\', \'experiment_alias\', \'file_name\', \'file_format\']\n+runs_dict = extract_data(xl_sheet, run_cols)\n+\n+# WRITE HEADERS TO TABLES\n+studies_table = open(pathlib.Path(args.out_path) / \'studies.tsv\', \'w\')\n+studies_table.write(\'\\t\'.join([\'alias\', \'status\', \'accession\', \'title\', \'study_type\',\n+ '..b' \'platform\', \'instrument_model\', \'submission_date\']) + \'\\n\')\n+\n+runs_table = open(pathlib.Path(args.out_path) / \'runs.tsv\', \'w\')\n+runs_table.write(\'\\t\'.join([\'alias\', \'status\', \'accession\', \'experiment_alias\', \'file_name\',\n+ \'file_format\', \'file_checksum\', \'submission_date\']) + \'\\n\')\n+action = args.action\n+\n+# WRITE DICTIONARIES TO TABLE FILES\n+\n+# ADD A TIMESTAMP TO THE ALIAS? SEEMS LIKE ENA REQUIRES ALL ENTRIES FOR A WEBIN TO HAVE UNIQUE IDS?\n+# dt_oobj = datetime.now(tz=None)\n+# timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")\n+for study_alias, study in studies_dict.items():\n+ # study_alias = study_alias + \'_\' + timestamp\n+ studies_table.write(\'\\t\'.join([study_alias, action, \'ENA_accession\', study[\'title\'],\n+ study[\'study_type\'], study[\'study_abstract\'], \'\',\n+ \'ENA_submission_data\']) + \'\\n\') # assuming no pubmed_id\n+for sample_alias, sample in samples_dict.items():\n+ # sample_alias = sample_alias + \'_\' + timestamp\n+ if args.viral_submission:\n+ if sample[\'collector name\'] == \'\':\n+ sample[\'collector name\'] = \'unknown\'\n+ samples_table.write(\'\\t\'.join([sample_alias, action, \'ena_accession\', sample[\'title\'],\n+ sample[\'scientific_name\'], \'tax_id_updated_by_ENA\',\n+ sample[\'sample_description\'], sample[\'collection date\'],\n+ sample[\'geographic location (country and/or sea)\'],\n+ sample[\'host common name\'], \'host subject id\',\n+ sample[\'host health state\'], sample[\'host sex\'],\n+ sample[\'host scientific name\'], sample[\'collector name\'],\n+ sample[\'collecting institution\'], sample[\'isolate\'],\n+ \'ENA_submission_date\']) + \'\\n\')\n+ else:\n+ samples_table.write(\'\\t\'.join([sample_alias, action, \'ena_accession\', sample[\'title\'],\n+ sample[\'scientific_name\'], \'tax_id_updated_by_ENA\',\n+ sample[\'sample_description\']]) + \'\\n\')\n+ for exp_alias, exp in experiments_dict.items():\n+ # should I check here if any experiment has a study or sample alias that is incorrect?\n+ # (not listed in the samples or study dict)\n+ # process the experiments for this sample\n+ if exp[\'sample_alias\'] == sample_alias:\n+ lib_alias = \'library_\' + exp_alias + \'_\' + exp[\'sample_alias\']\n+ experiments_table.write(\'\\t\'.join([exp_alias, action, \'accession_ena\', exp[\'title\'],\n+ exp[\'study_alias\'], sample_alias,\n+ exp[\'design_description\'], lib_alias,\n+ exp[\'library_strategy\'], exp[\'library_source\'],\n+ exp[\'library_selection\'],\n+ exp[\'library_layout\'].lower(),\n+ str(int(exp[\'insert_size\'])),\n+ exp[\'library_construction_protocol\'],\n+ exp[\'platform\'], exp[\'instrument_model\'],\n+ \'submission_date_ENA\']) + \'\\n\')\n+ for run_alias, run in runs_dict.items():\n+ if run[\'experiment_alias\'] == exp_alias:\n+ runs_table.write(\'\\t\'.join([run_alias, action, \'ena_run_accession\', exp_alias,\n+ run[\'file_name\'], FILE_FORMAT, \'file_checksum\',\n+ \'submission_date_ENA\']) + \'\\n\')\n+studies_table.close()\n+samples_table.close()\n+experiments_table.close()\n+runs_table.close()\n' |
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| diff -r 000000000000 -r 382518f24d6d samples_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samples_macros.xml Sat Nov 28 09:45:44 2020 +0000 |
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| b'@@ -0,0 +1,191 @@\n+<macros>\n+\n+ <xml name="table_inputs_macro">\n+ <conditional name="input_format_conditional">\n+ <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">\n+ <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option>\n+ <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>\n+ <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>\n+ </param>\n+ <when value="excel_tables">\n+ <param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />\n+ <param name="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>\n+ <param name="xlsx_file" type="data" format="xlsx" />\n+ <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/>\n+ </when>\n+ <when value="user_generated_tables">\n+ <param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />\n+ <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/>\n+ <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/>\n+ <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>\n+ <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>\n+ <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>\n+ </when>\n+ <when value="build_tables">\n+ <param name="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>\n+ <conditional name="conditional_viral_metadata">\n+ <param name="viral_sample" type="boolean" label="Does your submission contains viral samples?" />\n+ <when value="true">\n+ <expand macro="viral_samples" />\n+ </when>\n+ <when value="false">\n+ <expand macro="nonviral_samples" />\n+ </when>\n+ </conditional>\n+ </when>\n+ </conditional>\n+ <param name="center" type="text" optional="False" label="Affiliation center"/>\n+ </xml>\n+ <xml name="viral_samples">\n+ <repeat name="rep_study" title="Study" min="1">\n+ <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>\n+ <param name="study_abstract" type="text" optional="True" label="Please provide an abstract'..b'+ <repeat name="rep_sample" title="Samples associated with this study" min="1" >\n+ <param name="sample_title" type="text" label="Sample title"/>\n+ <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>\n+ <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>\n+ <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />\n+ <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >\n+ <param name="experiment_title" type="text" label="Specify an experiment title" />\n+ <param name="experiment_design" type="text" label="Describe the experiment design" />\n+ <param name="library_strategy" type="select" label="Library strategy" help="The\xc2\xa0library\xc2\xa0strategy\xc2\xa0specifies\xc2\xa0the\xc2\xa0sequencing\xc2\xa0technique\xc2\xa0intended\xc2\xa0for\xc2\xa0this\xc2\xa0library">\n+ <options from_data_table="library_strategy">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param name="library_source" type="select" label="Select library source" help="The\xc2\xa0library\xc2\xa0source\xc2\xa0specifies\xc2\xa0the\xc2\xa0type\xc2\xa0of\xc2\xa0source\xc2\xa0material\xc2\xa0that\xc2\xa0is\xc2\xa0being\xc2\xa0sequenced">\n+ <options from_data_table="library_source">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param name="library_selection" type="select" label="Library selection" help="The\xc2\xa0library\xc2\xa0selection\xc2\xa0specifies\xc2\xa0whether\xc2\xa0any\xc2\xa0method\xc2\xa0was\xc2\xa0used\xc2\xa0to\xc2\xa0select\xc2\xa0for\xc2\xa0or\xc2\xa0against,\xc2\xa0enrich,\xc2\xa0or\xc2\xa0screen\xc2\xa0the\xc2\xa0material\xc2\xa0being\xc2\xa0sequenced">\n+ <options from_data_table="library_selection">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param name="library_layout" type="select" label="Library layout">\n+ <options from_data_table="library_layout">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>\n+ <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>\n+ <param name="platform" type="select" label="Select the sequencing platform used">\n+ <option value="LS454">LS454</option>\n+ <option value="ILLUMINA">Illumina</option>\n+ <option value="HELICOS">Helicos</option>\n+ <option value="ABI_SOLID">ABI Solid</option>\n+ <option value="COMPLETE_GENOMICS">Complete Genomics</option>\n+ <option value="BGISEQ">BGI Seq</option>\n+ <option value="OXFORD_NANOPORE">Oxford Nanopore</option>\n+ <option value="PACBIO_SMRT">PacBio</option>\n+ <option value="ION_TORRENT">Ion Torrent</option>\n+ <option value="CAPILLARY">Capillary sequencing</option>\n+ </param>\n+ <param name="instrument_model" type="select" label="Instrument model">\n+ <options from_data_table="instrument_model">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >\n+ <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>\n+ </repeat>\n+ </repeat>\n+ </repeat>\n+ </repeat>\n+ </xml>\n+</macros>\n' |
| b |
| diff -r 000000000000 -r 382518f24d6d test-data/1.fastqsanger.gz |
| b |
| Binary file test-data/1.fastqsanger.gz has changed |
| b |
| diff -r 000000000000 -r 382518f24d6d test-data/metadata_test_nonviral.xlsx |
| b |
| Binary file test-data/metadata_test_nonviral.xlsx has changed |
| b |
| diff -r 000000000000 -r 382518f24d6d test-data/metadata_test_viral.xlsx |
| b |
| Binary file test-data/metadata_test_viral.xlsx has changed |
| b |
| diff -r 000000000000 -r 382518f24d6d test-data/sample.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.fq Sat Nov 28 09:45:44 2020 +0000 |
| b |
| b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACC'..b'FHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...//////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////.\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\n++\n+AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/\n' |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/geographic_location_1.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/geographic_location_1.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,279 @@ +not applicable +not collected +not provided +restricted access +Afghanistan +Albania +Algeria +American Samoa +Andorra +Angola +Anguilla +Antarctica +Antigua and Barbuda +Arctic Ocean +Argentina +Armenia +Aruba +Ashmore and Cartier Islands +Atlantic Ocean +Australia +Austria +Azerbaijan +Bahamas +Bahrain +Baker Island +Baltic Sea +Bangladesh +Barbados +Bassas da India +Belarus +Belgium +Belize +Benin +Bermuda +Bhutan +Bolivia +Borneo +Bosnia and Herzegovina +Botswana +Bouvet Island +Brazil +British Virgin Islands +Brunei +Bulgaria +Burkina Faso +Burundi +Cambodia +Cameroon +Canada +Cape Verde +Cayman Islands +Central African Republic +Chad +Chile +China +Christmas Island +Clipperton Island +Cocos Islands +Colombia +Comoros +Cook Islands +Coral Sea Islands +Costa Rica +Cote d'Ivoire +Croatia +Cuba +Curacao +Cyprus +Czech Republic +Democratic Republic of the Congo +Denmark +Djibouti +Dominica +Dominican Republic +East Timor +Ecuador +Egypt +El Salvador +Equatorial Guinea +Eritrea +Estonia +Ethiopia +Europa Island +Falkland Islands (Islas Malvinas) +Faroe Islands +Fiji +Finland +France +French Guiana +French Polynesia +French Southern and Antarctic Lands +Gabon +Gambia +Gaza Strip +Georgia +Germany +Ghana +Gibraltar +Glorioso Islands +Greece +Greenland +Grenada +Guadeloupe +Guam +Guatemala +Guernsey +Guinea +Guinea-Bissau +Guyana +Haiti +Heard Island and McDonald Islands +Honduras +Hong Kong +Howland Island +Hungary +Iceland +India +Indian Ocean +Indonesia +Iran +Iraq +Ireland +Isle of Man +Israel +Italy +Jamaica +Jan Mayen +Japan +Jarvis Island +Jersey +Johnston Atoll +Jordan +Juan de Nova Island +Kazakhstan +Kenya +Kerguelen Archipelago +Kingman Reef +Kiribati +Kosovo +Kuwait +Kyrgyzstan +Laos +Latvia +Lebanon +Lesotho +Liberia +Libya +Liechtenstein +Lithuania +Luxembourg +Macau +Macedonia +Madagascar +Malawi +Malaysia +Maldives +Mali +Malta +Marshall Islands +Martinique +Mauritania +Mauritius +Mayotte +Mediterranean Sea +Mexico +Micronesia +Midway Islands +Moldova +Monaco +Mongolia +Montenegro +Montserrat +Morocco +Mozambique +Myanmar +Namibia +Nauru +Navassa Island +Nepal +Netherlands +New Caledonia +New Zealand +Nicaragua +Niger +Nigeria +Niue +Norfolk Island +North Korea +North Sea +Northern Mariana Islands +Norway +Oman +Pacific Ocean +Pakistan +Palau +Palmyra Atoll +Panama +Papua New Guinea +Paracel Islands +Paraguay +Peru +Philippines +Pitcairn Islands +Poland +Portugal +Puerto Rico +Qatar +Republic of the Congo +Reunion +Romania +Ross Sea +Russia +Rwanda +Saint Helena +Saint Kitts and Nevis +Saint Lucia +Saint Pierre and Miquelon +Saint Vincent and the Grenadines +Samoa +San Marino +Sao Tome and Principe +Saudi Arabia +Senegal +Serbia +Seychelles +Sierra Leone +Singapore +Sint Maarten +Slovakia +Slovenia +Solomon Islands +Somalia +South Africa +South Georgia and the South Sandwich Islands +South Korea +Southern Ocean +Spain +Spratly Islands +Sri Lanka +Sudan +Suriname +Svalbard +Swaziland +Sweden +Switzerland +Syria +Taiwan +Tajikistan +Tanzania +Tasman Sea +Thailand +Togo +Tokelau +Tonga +Trinidad and Tobago +Tromelin Island +Tunisia +Turkey +Turkmenistan +Turks and Caicos Islands +Tuvalu +USA +Uganda +Ukraine +United Arab Emirates +United Kingdom +Uruguay +Uzbekistan +Vanuatu +Venezuela +Viet Nam +Virgin Islands +Wake Island +Wallis and Futuna +West Bank +Western Sahara +Yemen +Zambia +Zimbabwe |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/host_health_state_1.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/host_health_state_1.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,6 @@ +not applicable +diseased +healthy +not provided +not collected +restricted access |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/host_sex_1.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/host_sex_1.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,9 @@ +other +not applicable +not provided +neuter +not collected +female +restricted access +male +hermaphrodite |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/instrument_model.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/instrument_model.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,58 @@ +minION +GridION +PromethION +454 GS +454 GS 20 +454 GS FLX +454 GS FLX+ +454 GS FLX Titanium +454 GS Junior +Illumina Genome Analyzer +Illumina Genome Analyzer II +Illumina Genome Analyzer IIx +Illumina HiSeq 1000 +Illumina HiSeq 1500 +Illumina HiSeq 2000 +Illumina HiSeq 2500 +Illumina HiSeq 3000 +Illumina HiSeq 4000 +Illumina iSeq 100 +Illumina HiScanSQ +Illumina NextSeq 500 +Illumina NextSeq 550 +Illumina NovaSeq 6000 +Illumina HiSeq X Five +Illumina HiSeq X Ten +Illumina MiSeq +Illumina MiniSeq +AB SOLiD System +AB SOLiD System 2.0 +AB SOLiD System 3.0 +AB SOLiD 3 Plus System +AB SOLiD 4 System +AB SOLiD 4hq System +AB SOLiD PI System +AB 5500 Genetic Analyzer +AB 5500xl Genetic Analyzer +AB 5500xl-W Genetic Analysis System +Ion Torrent PGM +Ion Torrent Proton +Ion Torrent S5 +Ion Torrent S5 XL +Complete Genomics +PacBio RS +PacBio RS II +Sequel +Sequel II +AB 3730xL Genetic Analyzer +AB 3730 Genetic Analyzer +AB 3500xL Genetic Analyzer +AB 3500 Genetic Analyzer +AB 3130xL Genetic Analyzer +AB 3130 Genetic Analyzer +AB 310 Genetic Analyzer +BGISEQ-500 +DNBSEQ-T7 +DNBSEQ-G400 +DNBSEQ-G50 +DNBSEQ-G400 FAST |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/library_layout.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/library_layout.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +SINGLE +PAIRED |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/library_selection.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/library_selection.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,27 @@ +RANDOM +PCR +RANDOM PCR +RT-PCR +HMPR +MF +repeat fractionation +size fractionation +MSLL +cDNA +ChIP +MNase +DNase +Hybrid Selection +Reduced Representation +Restriction Digest +5-methylcytidine antibody +MBD2 protein methyl-CpG binding domain +CAGE +RACE +MDA +padlock probes capture method +Oligo-dT +Inverse rRNA selection +ChIP-Seq +other +unspecified |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/library_source.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/library_source.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,7 @@ +GENOMIC +TRANSCRIPTOMIC +METAGENOMIC +METATRANSCRIPTOMIC +SYNTHETIC +VIRAL RNA +OTHER |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/library_strategy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/library_strategy.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,38 @@ +WGS +WGA +WXS +RNA-Seq +ssRNA-seq +miRNA-Seq +ncRNA-Seq +FL-cDNA +EST +Hi-C +ATAC-seq +WCS +RAD-Seq +CLONE +POOLCLONE +AMPLICON +CLONEEND +FINISHING +ChIP-Seq +MNase-Seq +DNase-Hypersensitivity +Bisulfite-Seq +CTS +MRE-Seq +MeDIP-Seq +MBD-Seq +Tn-Seq +VALIDATION +FAIRE-seq +SELEX +RIP-Seq +ChIA-PET +Synthetic-Long-Read +Targeted-Capture +Tethered Chromatin Conformation Capture +ChM-Seq +GBS +OTHER |
| b |
| diff -r 000000000000 -r 382518f24d6d tool-data/study_type.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/study_type.loc.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,14 @@ +Whole Genome Sequencing +Metagenomics +Transcriptome Analysis +Resequencing +Epigenetics +Synthetic Genomics +Forensic or Paleo-genomics +Gene Regulation Study +Cancer Genomics +Population Genomics +RNASeq +Exome Sequencing +Pooled Clone Sequencing +Transcriptome Sequencing |
| b |
| diff -r 000000000000 -r 382518f24d6d tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,13 @@ +<?xml version="1.0"?> + <tables> + <table name="study_type" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/study_type.loc" /></table> + <table name="library_layout" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_layout.loc" /></table> + <table name="library_selection" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_selection.loc" /></table> + <table name="instrument_model" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/instrument_model.loc" /></table> + <table name="library_source" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_source.loc" /></table> + <table name="library_strategy" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_strategy.loc" /></table> + <table name="geographic_location_1" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/geographic_location_1.loc" /></table> + <table name="host_sex_1" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/host_sex_1.loc" /></table> + <table name="host_health_state_1" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/host_health_state_1.loc" /></table> + </tables> + |
| b |
| diff -r 000000000000 -r 382518f24d6d tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sat Nov 28 09:45:44 2020 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini --> +<tables> + <table name="study_type" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/study_type.loc.sample" /></table> + <table name="library_layout" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/library_layout.loc.sample" /></table> + <table name="library_selection" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/library_selection.loc.sample" /></table> + <table name="instrument_model" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/instrument_model.loc.sample" /></table> + <table name="library_source" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/library_source.loc.sample" /></table> + <table name="library_strategy" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/library_strategy.loc.sample" /></table> + <table name="geographic_location_1" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/geographic_location_1.loc.sample" /></table> + <table name="host_sex_1" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/host_sex_1.loc.sample" /></table> + <table name="host_health_state_1" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/host_health_state_1.loc.sample" /></table> +</tables> |