| Previous changeset 9:a62c4a11a67d (2022-11-10) Next changeset 11:f803a68fc9e5 (2024-03-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3 |
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modified:
ena_upload.xml extract_tables.py samples_macros.xml test-data/metadata_test_nonviral.xlsx test-data/metadata_test_nonviral_1_run.xlsx tool-data/geographic_location_1.loc.sample tool-data/host_sex_1.loc.sample tool-data/instrument_model.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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README.rst tool-data/platform.loc.sample |
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README.md |
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| diff -r a62c4a11a67d -r 480d9e9d156b README.md --- a/README.md Thu Nov 10 15:18:00 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,31 +0,0 @@ -# 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 $GALAXY_ENA_SECRETS - -Alternatively, the admin can enable users to set their own credentials for this tool. -To enable it, make sure the file `config/user_preferences_extra_conf.yml` has the following section: - -``` - ena_webin_account: - description: Your ENA Webin account details - inputs: - - name: webin_id - label: ENA Webin ID - type: text - required: False - - name: password - label: Password - type: password - required: False -``` |
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| diff -r a62c4a11a67d -r 480d9e9d156b README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -0,0 +1,42 @@ +ENA-upload-cli wrapper +====================== + +Galaxy wrapper of the +`ena-upload-cli <https://github.com/usegalaxy-eu/ena-upload-cli>`__. +Templates that can be used in as input for the metadata can be found +`here <https://github.com/ELIXIR-Belgium/ENA-metadata-templates>`__ + +This tool is shipped in a ready to use Galaxy container found +`here <https://github.com/ELIXIR-Belgium/ena-upload-container>`__. + +Setting up credentials on Galaxy +-------------------------------- + +The admin of the server can set up global credentials through a file +with the format: + +.. code-block:: yaml + + username: webin_id + password: webin_password + +The path to this file must be exported as an environment variable called +$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: + +.. code-block:: yaml + + 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 a62c4a11a67d -r 480d9e9d156b ena_upload.xml --- a/ena_upload.xml Thu Nov 10 15:18:00 2022 +0000 +++ b/ena_upload.xml Fri Oct 27 19:44:40 2023 +0000 |
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| b'@@ -1,10 +1,11 @@\n-<tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT">\n+<tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT">\n <macros>\n- <token name="@VERSION@">0.6.1</token>\n+ <token name="@TOOL_VERSION@">0.6.3</token>\n+ <token name="@VERSION_SUFFIX@">0</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="@TOOL_VERSION@">ena-upload-cli</requirement>\n </requirements>\n <stdio>\n <regex match="Oops" source="stderr" level="fatal"/>\n@@ -47,7 +48,7 @@\n #if $action_options.input_format_conditional.input_format == "excel_tables":\n ln -s \'$action_options.input_format_conditional.xlsx_file\' ./xlsx_input.xlsx &&\n #end if\n-#if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":\n+#if $action_options.test_submit_parameters.dry_run == "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@@ -57,7 +58,7 @@\n credentials_path=\\${GALAXY_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+ 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@@ -80,7 +81,7 @@\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- #if $action_options.input_format_conditional.add_extension == "true":\n+ #if $action_options.input_format_conditional.add_extension == "True":\n #set $extension = \'.fastq\'\n #else\n #set $extension = \'\'\n@@ -90,7 +91,7 @@\n #set $safename_reads_file = $safename_reads_file + $extension + \'.gz\'\n gzip -c \'$file\' > $safename_reads_file &&\n #else:\n- #if $action_options.input_format_conditional.add_extension == "true":\n+ #if $action_options.input_format_conditional.add_extension == "True":\n #if $file.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n #set $compression = \'.gz\' \n #elif $file.is_of_type(\'fastqsanger.bz2\', \'fastq.bz2\'):\n@@ -148,14 +149,14 @@\n #set $safename_reads_file = re.sub(\'[^\\w\\-_\\.]\', \'_\', $file.element_identifier)\n #if $file.is_of_type(\'fastq\', \'fastqsanger\'):\n ## always compress add the gz extension\n- #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":\n+ #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":\n #set $safename_reads_file = $safename_reads_file + \'.fastq.gz\'\n #else\n #set $safename_reads_file = $safename_reads_file + \'.gz\'\n- #end if \n+ #end if\n gzip -c \'$file\' > $safename_reads_file &&\n #else\n- #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":\n+ #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":\n #if $file.is_of_type(\'fastq.gz\','..b'name="add_extension" value="False"/>\n <param name="input_format" value="build_tables"/>\n <conditional name="conditional_viral_metadata">\n- <param name="viral_sample" value="true"/>\n+ <param name="viral_sample" value="True"/>\n <repeat name="rep_study">\n <param name="study_title" value="Test study title"/>\n <param name="study_abstract" value="Test study abstract"/>\n@@ -822,17 +777,17 @@\n <has_text_matching expression="--checklist ERC000033"/>\n </assert_command>\n </test>\n- <!--Test 9: modify option and auto compression - viral submission - User input metadata-->\n- <test expect_failure="false">\n+ <!--Test 8: modify option and auto compression - viral submission - User input metadata-->\n+ <test expect_failure="False" expect_num_outputs="5">\n <conditional name="action_options">\n <param name="action" value="modify"/>\n <section name="test_submit_parameters">\n- <param name="submit_dev" value="false" />\n- <param name="dry_run" value="true" />\n+ <param name="submit_dev" value="False" />\n+ <param name="dry_run" value="True" />\n </section>\n <param name="test_submit" value="True"/>\n <conditional name="input_format_conditional">\n- <param name="add_extension" value="fasle"/>\n+ <param name="add_extension" value="False"/>\n <param name="input_format" value="build_tables"/>\n <conditional name="conditional_viral_metadata">\n <param name="viral_sample" value="True"/>\n@@ -869,7 +824,7 @@\n <param name="instrument_model" value="Illumina HiSeq 4000"/>\n <repeat name="rep_runs">\n <param name="run_base_name" value="run_from_hospital_X"/>\n- <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/>\n+ <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>\n </repeat>\n </repeat>\n </repeat>\n@@ -880,7 +835,7 @@\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\'"/>\n+ <has_text_matching expression="--data \'1.fastqsanger.gz\' \'2.fastqsanger.gz\'"/>\n <has_text_matching expression="--action \'modify\' --center \'Some research center\'"/>\n <has_text_matching expression="--checklist ERC000033"/>\n <not_has_text text="add" />\n@@ -889,9 +844,9 @@\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://github.com/ELIXIR-Belgium/ENA-metadata-templates\n+ The input metadata can be submitted following the tabular format of the templates or their excel spreadsheet equivalent in https://github.com/ELIXIR-Belgium/ENA-metadata-templates. This template repo provides ready to use sheets for every ENA sample checklist and is automatically updated.\n ]]></help>\n <citations>\n+ <citation type="doi">doi:10.1093/bioinformatics/btab421</citation>\n </citations>\n </tool>\n' |
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| diff -r a62c4a11a67d -r 480d9e9d156b extract_tables.py --- a/extract_tables.py Thu Nov 10 15:18:00 2022 +0000 +++ b/extract_tables.py Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -40,21 +40,20 @@ for study_index, study in enumerate(studies_dict): study_alias = 'study_' + str(study_index) + '_' + timestamp studies_table.write('\t'.join([study_alias, action, study['title'], - study['type'], study['abstract'], study['pubmed_id'], - ])) - if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample + study['type'], study['abstract'], study['pubmed_id']])) + if "host_subject_id" in study['samples'][0].keys(): # sample belongs to a viral sample samples_table.write('\t'.join(['alias', 'status', 'title', 'scientific_name', 'taxon_id', 'sample_description', 'collection date', 'geographic location (country and/or sea)', 'host common name', 'host subject id', 'host health state', 'host sex', 'host scientific name', - 'collector name', 'collecting institution', 'isolate', - ]) + '\n') + 'collector name', 'collecting institution', 'isolate']) + '\n') else: samples_table.write('\t'.join(['alias', 'status', 'title', 'scientific_name', - 'taxon_id', 'sample_description']) + '\n') + 'taxon_id', 'sample_description', 'collection date', + 'geographic location (country and/or sea)']) + '\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 "host_subject_id" 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, sample['title'], @@ -64,12 +63,13 @@ sample['host_subject_id'], sample['host_health_state'], sample['host_sex'], sample['host_scientific_name'], sample['collector_name'], - sample['collecting_institution'], sample['isolate'], + sample['collecting_institution'], sample['isolate'] ]) + '\n') else: samples_table.write('\t'.join([sample_alias, action, sample['title'], sample['tax_name'], sample['tax_id'], - sample['description']]) + '\n') + sample['description'], sample['collection_date'], + sample['geo_location']]) + '\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) @@ -79,8 +79,7 @@ exp['library_source'], exp['library_selection'], exp['library_layout'].lower(), exp['insert_size'], exp['library_construction_protocol'], - exp['platform'], exp['instrument_model'], - ]) + '\n') + exp['platform'], exp['instrument_model']]) + '\n') run_index = 0 # exp['runs'] is a list of lists for (base_run, run_files) in exp['runs']: |
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| diff -r a62c4a11a67d -r 480d9e9d156b samples_macros.xml --- a/samples_macros.xml Thu Nov 10 15:18:00 2022 +0000 +++ b/samples_macros.xml Fri Oct 27 19:44:40 2023 +0000 |
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| b'@@ -44,9 +44,9 @@\n </param>\n </xml>\n <xml name="test_submit_section">\n- <section name="test_submit_parameters" expanded="true" title="Testing options">\n- <param name="submit_dev" type="boolean" truevalue="true" falsevalue="false" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" />\n- <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>\n+ <section name="test_submit_parameters" expanded="True" title="Testing options">\n+ <param name="submit_dev" type="boolean" truevalue="True" falsevalue="False" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" />\n+ <param name="dry_run" type="boolean" truevalue="True" falsevalue="False" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>\n </section>\n </xml>\n <xml name="run_inputs_macro">\n@@ -57,7 +57,7 @@\n </param>\n <when value="multiple_selection_list">\n <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>\n- <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run\'s files names defined in the metadata"/>\n+ <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="Select individual datasets or a dataset collection" help="Names should match the compressed run\'s files names defined in the metadata"/>\n </when>\n <when value="paired_list">\n <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run\'s files names defined in the metadata" />\n@@ -68,7 +68,7 @@\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 template</option>\n- <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>\n+ <option value="build_tables" selected="False">Interactive generation of the study structure (only 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@@ -81,19 +81,22 @@\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 '..b'l" 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="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>\n- <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>\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 library strategy specifies the sequencing technique intended for this library">\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 library source specifies the type of source material that is being sequenced">\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 library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">\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+ <options from_data_table="platform">\n+ <column name="value" index="0"/>\n+ </options>\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="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>\n+ <param name="upload_files" type="data" format="fastq,fastqsanger,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- </repeat>\n </xml>\n </macros>\n' |
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| diff -r a62c4a11a67d -r 480d9e9d156b test-data/metadata_test_nonviral.xlsx |
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| Binary file test-data/metadata_test_nonviral.xlsx has changed |
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| diff -r a62c4a11a67d -r 480d9e9d156b test-data/metadata_test_nonviral_1_run.xlsx |
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| Binary file test-data/metadata_test_nonviral_1_run.xlsx has changed |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/geographic_location_1.loc.sample --- a/tool-data/geographic_location_1.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/geographic_location_1.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -1,7 +1,3 @@ -not applicable -not collected -not provided -restricted access Afghanistan Albania Algeria @@ -277,3 +273,15 @@ Yemen Zambia Zimbabwe +missing: control sample +missing: data agreement established pre-2023 +missing: endangered species +missing: human-identifiable +missing: lab stock +missing: sample group +missing: synthetic construct +missing: third party data +not applicable +not collected +not provided +restricted access |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/host_sex_1.loc.sample --- a/tool-data/host_sex_1.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/host_sex_1.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -1,9 +1,17 @@ -other +female +hermaphrodite +male +missing: control sample +missing: data agreement established pre-2023 +missing: endangered species +missing: human-identifiable +missing: lab stock +missing: sample group +missing: synthetic construct +missing: third party data +neuter not applicable -not provided -neuter not collected -female +not provided +other restricted access -male -hermaphrodite |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/instrument_model.loc.sample --- a/tool-data/instrument_model.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/instrument_model.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -1,58 +1,75 @@ -minION -GridION -PromethION 454 GS 454 GS 20 454 GS FLX +454 GS FLX Titanium 454 GS FLX+ -454 GS FLX Titanium 454 GS Junior +AB 310 Genetic Analyzer +AB 3130 Genetic Analyzer +AB 3130xL Genetic Analyzer +AB 3500 Genetic Analyzer +AB 3500xL Genetic Analyzer +AB 3730 Genetic Analyzer +AB 3730xL Genetic Analyzer +AB 5500 Genetic Analyzer +AB 5500xl Genetic Analyzer +AB 5500xl-W Genetic Analysis System +AB SOLiD 3 Plus System +AB SOLiD 4 System +AB SOLiD 4hq System +AB SOLiD PI System +AB SOLiD System +AB SOLiD System 2.0 +AB SOLiD System 3.0 +BGISEQ-50 +BGISEQ-500 +Complete Genomics +DNBSEQ-G400 +DNBSEQ-G400 FAST +DNBSEQ-G50 +DNBSEQ-T7 +Element AVITI +GridION +Helicos HeliScope +HiSeq X Five +HiSeq X Ten Illumina Genome Analyzer Illumina Genome Analyzer II Illumina Genome Analyzer IIx +Illumina HiScanSQ 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 HiSeq X 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 +Illumina NovaSeq 6000 +Illumina NovaSeq X +Illumina iSeq 100 +Ion GeneStudio S5 +Ion GeneStudio S5 Plus +Ion GeneStudio S5 Prime +Ion Torrent Genexus Ion Torrent PGM Ion Torrent Proton Ion Torrent S5 Ion Torrent S5 XL -Complete Genomics +MGISEQ-2000RS +MinION +NextSeq 1000 +NextSeq 2000 +NextSeq 500 +NextSeq 550 +Onso PacBio RS PacBio RS II +PromethION +Revio 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 +Sequel IIe +UG 100 +unspecified |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/library_selection.loc.sample --- a/tool-data/library_selection.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/library_selection.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -8,7 +8,14 @@ size fractionation MSLL cDNA +cDNA_randomPriming +cDNA_oligo_dT +PolyA +Oligo-dT +Inverse rRNA +Inverse rRNA selection ChIP +ChIP-Seq MNase DNase Hybrid Selection @@ -20,8 +27,5 @@ RACE MDA padlock probes capture method -Oligo-dT -Inverse rRNA selection -ChIP-Seq other unspecified |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/library_source.loc.sample --- a/tool-data/library_source.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/library_source.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -1,5 +1,7 @@ GENOMIC +GENOMIC SINGLE CELL TRANSCRIPTOMIC +TRANSCRIPTOMIC SINGLE CELL METAGENOMIC METATRANSCRIPTOMIC SYNTHETIC |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/library_strategy.loc.sample --- a/tool-data/library_strategy.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/library_strategy.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -3,6 +3,7 @@ WXS RNA-Seq ssRNA-seq +snRNA-seq miRNA-Seq ncRNA-Seq FL-cDNA @@ -33,6 +34,8 @@ Synthetic-Long-Read Targeted-Capture Tethered Chromatin Conformation Capture +NOMe-Seq ChM-Seq GBS +Ribo-Seq OTHER |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/platform.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/platform.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
| b |
| @@ -0,0 +1,13 @@ +LS454 +ILLUMINA +HELICOS +ABI_SOLID +COMPLETE_GENOMICS +BGISEQ +OXFORD_NANOPORE +PACBIO_SMRT +ION_TORRENT +CAPILLARY +DNBSEQ +ELEMENT +ULTIMA |
| b |
| diff -r a62c4a11a67d -r 480d9e9d156b tool-data/study_type.loc.sample --- a/tool-data/study_type.loc.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool-data/study_type.loc.sample Fri Oct 27 19:44:40 2023 +0000 |
| b |
| @@ -12,3 +12,4 @@ Exome Sequencing Pooled Clone Sequencing Transcriptome Sequencing +Other |
| b |
| diff -r a62c4a11a67d -r 480d9e9d156b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Nov 10 15:18:00 2022 +0000 +++ b/tool_data_table_conf.xml.sample Fri Oct 27 19:44:40 2023 +0000 |
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| @@ -4,10 +4,10 @@ <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="platform" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/platform.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> - |
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| diff -r a62c4a11a67d -r 480d9e9d156b tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Thu Nov 10 15:18:00 2022 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 27 19:44:40 2023 +0000 |
| b |
| @@ -4,6 +4,7 @@ <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="platform" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__HERE__}/tool-data/platform.loc.sample" /></table> <table name="library_source" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="${__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> |