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Revision: 9:a62c4a11a67d

Repository 'ena_upload'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ena_upload

ENA Upload tool tool metadata

Miscellaneous

Name: ENA Upload tool

Description:

Id: ena_upload

Guid: toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.6.1

Version: 0.6.1

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.6.3+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.6.1 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.6.0

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

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)

Requirements:

name

version

type

ena-upload-cli

0.6.1

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|checklist_id: ERC000033
action_options|input_format_conditional|xlsx_file: metadata_test_viral.xlsx
action_options|input_format_conditional|run_input_format_conditional|add_extension: False
action_options|input_format_conditional|run_input_format_conditional|data: ['C030_exp5_clean.fastq', 'C053_exp5_clean.fastq', 'C026_exp5_clean.fastq', 'C067_exp5_clean.fastq']
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
C030_exp5_clean.fastq
C053_exp5_clean.fastq
C026_exp5_clean.fastq
C067_exp5_clean.fastq
value

Test-2

action_options|test_submit_parameters|submit_dev: False
action_options|test_submit_parameters|dry_run: True
action_options|input_format_conditional|checklist_id: ERC000033
action_options|input_format_conditional|xlsx_file: metadata_test_viral_optional_columns.xlsx
action_options|input_format_conditional|run_input_format_conditional|add_extension: False
action_options|input_format_conditional|run_input_format_conditional|data: ['C030_exp5_clean.fastq', 'C053_exp5_clean.fastq', 'C026_exp5_clean.fastq', 'C067_exp5_clean.fastq']
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
name: value

metadata_test_viral_optional_columns.xlsx
C030_exp5_clean.fastq
C053_exp5_clean.fastq
C026_exp5_clean.fastq
C067_exp5_clean.fastq
value

Test-3

action_options|test_submit_parameters|submit_dev: False
action_options|test_submit_parameters|dry_run: True
action_options|input_format_conditional|checklist_id: ERC000011
action_options|input_format_conditional|xlsx_file: metadata_test_nonviral_1_run.xlsx
action_options|input_format_conditional|run_input_format_conditional|add_extension: True
action_options|input_format_conditional|run_input_format_conditional|data: sample_no_extension
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_1_run.xlsx
sample_no_extension
value

Test-4

action_options|test_submit_parameters|submit_dev: False
action_options|test_submit_parameters|dry_run: False
action_options|input_format_conditional|checklist_id: ERC000011
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|idempotent: True
action_options|test_submit_parameters|submit_dev: False
action_options|test_submit_parameters|dry_run: False
action_options|input_format_conditional|checklist_id: ERC000011
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-6

action_options|test_submit_parameters|submit_dev: False
action_options|test_submit_parameters|dry_run: 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: 2697049
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-7

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: 2697049
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-8

action_options|test_submit_parameters|submit_dev: True
action_options|test_submit_parameters|dry_run: True
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: 2697049
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: False
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: True
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: 2697049
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-10

action_options|test_submit_parameters|submit_dev: False
action_options|test_submit_parameters|dry_run: True
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: 2697049
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
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

1.fastqsanger.gz