Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.5.3 |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.4.3 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.4.1 |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.3 |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.2 |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.1 |
toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3 |
ena_upload |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
ena-upload-cli | 0.4.3 | package |
xlrd | 1.2.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: True action_options|input_format_conditional|viral_submission: True action_options|input_format_conditional|xlsx_file: metadata_test_viral.xlsx action_options|input_format_conditional|run_input_format_conditional|add_extension: True action_options|input_format_conditional|run_input_format_conditional|data: sample.fq action_options|input_format_conditional|run_input_format_conditional|run_input_format: multiple_selection_list action_options|input_format_conditional|input_format: excel_tables action_options|center: Some research center action_options|action: add |
name: value name: value name: value name: value |
metadata_test_viral.xlsx sample.fq value |
Test-2 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: True action_options|input_format_conditional|viral_submission: True action_options|input_format_conditional|xlsx_file: metadata_test_viral_optional_columns.xlsx action_options|input_format_conditional|run_input_format_conditional|add_extension: True action_options|input_format_conditional|run_input_format_conditional|data: sample.fq action_options|input_format_conditional|run_input_format_conditional|run_input_format: multiple_selection_list action_options|input_format_conditional|input_format: excel_tables action_options|center: Some research center action_options|action: add |
name: value name: value name: value name: value |
metadata_test_viral_optional_columns.xlsx sample.fq value |
Test-3 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: True action_options|input_format_conditional|viral_submission: False action_options|input_format_conditional|xlsx_file: metadata_test_nonviral.xlsx action_options|input_format_conditional|run_input_format_conditional|add_extension: True action_options|input_format_conditional|run_input_format_conditional|data: sample.fq action_options|input_format_conditional|run_input_format_conditional|run_input_format: multiple_selection_list action_options|input_format_conditional|input_format: excel_tables action_options|center: Some research center action_options|action: add |
name: value name: value name: value name: value |
metadata_test_nonviral.xlsx sample.fq value |
Test-4 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: False action_options|input_format_conditional|viral_submission: False action_options|input_format_conditional|xlsx_file: metadata_test_nonviral.xlsx action_options|input_format_conditional|run_input_format_conditional|paired_end_collection: list:paired collection action_options|input_format_conditional|run_input_format_conditional|run_input_format: paired_list action_options|input_format_conditional|input_format: excel_tables action_options|center: Some research center action_options|action: add |
metadata_test_nonviral.xlsx 1.fastqsanger.gz 2.fastqsanger.gz |
|
Test-5 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: True action_options|input_format_conditional|add_extension: True action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_title: Test study title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_abstract: Test study abstract action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_type: Epigenetics action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_pubmed_id: Test study pubmedID action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_title: Test Sample title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_description: Test Sample description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|scientific_name: Test Sample scientific name action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|tax_id: Test Sample tax_id action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_title: Test experiment title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_design: Test experiment design description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_strategy: CTS action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_source: GENOMIC action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_selection: PCR action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_layout: SINGLE action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|insert_size: 150 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_construction_protocol: Test library construction action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|platform: ILLUMINA action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|instrument_model: Illumina HiSeq 4000 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|upload_files: ['1.fastqsanger.gz', 'sample.fq'] action_options|input_format_conditional|conditional_viral_metadata|viral_sample: False action_options|input_format_conditional|input_format: build_tables action_options|center: Some research center action_options|action: add |
name: value name: value name: value name: value |
1.fastqsanger.gz sample.fq value |
Test-6 |
action_options|test_submit_parameters|submit_dev: True action_options|test_submit_parameters|dry_run: False action_options|input_format_conditional|add_extension: True action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_title: Test study title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_abstract: Test study abstract action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_type: Epigenetics action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_pubmed_id: Test study pubmedID action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_title: Test Sample title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_description: Test Sample description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|scientific_name: Test Sample scientific name action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|tax_id: Test Sample tax_id action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_title: Test experiment title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_design: Test experiment design description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_strategy: CTS action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_source: GENOMIC action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_selection: PCR action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_layout: SINGLE action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|insert_size: 150 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_construction_protocol: Test library construction action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|platform: ILLUMINA action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|instrument_model: Illumina HiSeq 4000 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|upload_files: ['1.fastqsanger.gz', 'sample.fq'] action_options|input_format_conditional|conditional_viral_metadata|viral_sample: False action_options|input_format_conditional|input_format: build_tables action_options|center: Some research center action_options|action: add |
1.fastqsanger.gz sample.fq |
|
Test-7 |
action_options|test_submit_parameters|submit_dev: True action_options|test_submit_parameters|dry_run: False action_options|test_submit: True action_options|input_format_conditional|add_extension: True action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_title: Test study title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_abstract: Test study abstract action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_type: Epigenetics action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_pubmed_id: Test study pubmedID action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_title: Test Sample title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_description: Test Sample description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|scientific_name: Test Sample scientific name action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|tax_id: Test Sample tax_id action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_title: Test experiment title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_design: Test experiment design description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_strategy: CTS action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_source: GENOMIC action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_selection: PCR action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_layout: SINGLE action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|insert_size: 150 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_construction_protocol: Test library construction action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|platform: ILLUMINA action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|instrument_model: Illumina HiSeq 4000 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|run_base_name: run_from_hospital_X action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|upload_files: ['sample.fq', 'sample.fq'] action_options|input_format_conditional|conditional_viral_metadata|viral_sample: False action_options|input_format_conditional|input_format: build_tables action_options|center: Some research center action_options|action: add |
sample.fq |
|
Test-8 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: False action_options|test_submit: True action_options|input_format_conditional|add_extension: False action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_title: Test study title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_abstract: Test study abstract action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_type: Epigenetics action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_pubmed_id: Test study pubmedID action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_title: Test Sample title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_description: Test Sample description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|scientific_name: Test Sample scientific name action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|tax_id: Test Sample tax_id action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|collection_date: 2020 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|geo_location_country: Belgium action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_common_name: Human action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_subject_id: Patient_001 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_health_state: healthy action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_sex: female action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_scientific_name: homo sapiens action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|collector_name: John The Collector action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|collecting_institution: Hospital 01 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|isolate: sample_001 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_title: Test experiment title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_design: Test experiment design description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_strategy: CTS action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_source: GENOMIC action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_selection: PCR action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_layout: SINGLE action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|insert_size: 150 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_construction_protocol: Test library construction action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|platform: ILLUMINA action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|instrument_model: Illumina HiSeq 4000 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|run_base_name: run_from_hospital_X action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|upload_files: ['1.fastqsanger.gz', '2.fastqsanger.gz'] action_options|input_format_conditional|conditional_viral_metadata|viral_sample: True action_options|input_format_conditional|input_format: build_tables action_options|center: Some research center action_options|action: add |
1.fastqsanger.gz 2.fastqsanger.gz |
|
Test-9 |
action_options|test_submit_parameters|submit_dev: False action_options|test_submit_parameters|dry_run: False action_options|test_submit: True action_options|input_format_conditional|add_extension: False action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_title: Test study title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_abstract: Test study abstract action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_type: Epigenetics action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|study_pubmed_id: Test study pubmedID action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_title: Test Sample title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|sample_description: Test Sample description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|scientific_name: Test Sample scientific name action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|tax_id: Test Sample tax_id action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|collection_date: 2020 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|geo_location_country: Belgium action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_common_name: Human action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_subject_id: Patient_001 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_health_state: healthy action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_sex: female action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|host_scientific_name: homo sapiens action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|collector_name: John The Collector action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|collecting_institution: Hospital 01 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|isolate: sample_001 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_title: Test experiment title action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|experiment_design: Test experiment design description action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_strategy: CTS action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_source: GENOMIC action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_selection: PCR action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_layout: SINGLE action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|insert_size: 150 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|library_construction_protocol: Test library construction action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|platform: ILLUMINA action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|instrument_model: Illumina HiSeq 4000 action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|run_base_name: run_from_hospital_X action_options|input_format_conditional|conditional_viral_metadata|rep_study_0|rep_sample_0|rep_experiment_0|rep_runs_0|upload_files: sample.fq action_options|input_format_conditional|conditional_viral_metadata|viral_sample: True action_options|input_format_conditional|input_format: build_tables action_options|center: Some research center action_options|action: modify |
sample.fq |