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Download Metadata ENA Program
The Download Metadata ENA program allows downloading the metadata associated with an ENA study project by collecting the information available in the ENA Browser and the data related to the project’s samples using the mg-tooolkit package (https://pypi.org/project/mg-toolkit/). A left join will be carried out, taking the PROJECT_ENA_browser.tsv file as reference. This program corresponds to the Collection Programs group. Exclusive for ENA Dataset Workflow.
Input Elements:
| Input | Type | Description |
|---|---|---|
PROJECT |
Parameter |
ENA Project Accession |
Output Elements:
| Output | Type | Description |
|---|---|---|
PROJECT_ENA_browser.tsv |
File |
ENA Technical Metadata (ENA Browser) |
PROJECT_mg-toolkit.tsv |
File |
ENA Samples Metadata (mg-toolkit) |
PROJECT_ENA_metadata.tsv |
File |
ENA Metadata Table |
The resulting PROJECT_ENA_metadata.tsv file is the one that will be used in the next workflow steps. Depending on whether or not additional metadata is available, the next workflow step will be performed with the Merge Metadata program or directly with the Check Metadata ENA program, respectively. To get a general idea of the following steps, check the workflow's diagram.
Usage:
download_metadata_ENA [-h] -p PROJECT [-o OUTPUT_DIRECTORY] [-x] [-v]
Options:
| Parameter | Description |
|---|---|
-h, --help |
Show help message and exit. |
-p, --project |
Project Accession. Indicate ENA Study Accession. |
-o, --output_directory |
Output Directory (Optional). Indicate the path to the Output Directory. Output files will be created in the current directory if not indicated. |
-x, --plain_text |
Plain Text Mode (Optional). If indicated, it will enable Plain Text mode, and text will appear without colors. |
-v, --version |
Show program's version number and exit. |
Commands:
- Download metadata with colored text stdout:
download_metadata_ENA -p PRJEB10949
- Download metadata with plain text stdout:
download_metadata_ENA -p PRJEB10949 --plain_text
- Download metadata in the specified directory (Example):
download_metadata_ENA -p PRJEB10949 -o Example
To see a full and detailed example of dataset curation, see the Tutorial Full Example page.