| Name | rcx-tk JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | None |
| Summary | This package adjusts and cleans the metadata file provided by a user. |
| upload_time | 2024-07-15 12:27:49 |
| maintainer | None |
| docs_url | None |
| author | Zargham Ahmad |
| requires_python | <4.0,>=3.11 |
| license | MIT |
| keywords |
metadata
alkanes
metabolomics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
## Badges
| fair-software.eu recommendations | |
| :-- | :-- |
| (1/5) code repository | [](https://github.com/RECETOX/rcx-tk) |
| (2/5) license | [](https://github.com/RECETOX/rcx-tk) |
| (3/4) citation | [](https://doi.org/<replace-with-created-DOI>) |
| (4/4) checklist | [](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
| howfairis | [](https://fair-software.eu) |
| **Other best practices** | |
| Static analysis | [](https://sonarcloud.io/dashboard?id=RECETOX_rcx-tk) |
| Coverage | [](https://sonarcloud.io/dashboard?id=RECETOX_rcx-tk) |
| Documentation | [](https://rcx-tk.readthedocs.io/en/latest/?badge=latest) |
| **GitHub Actions** | |
| Build | [](https://github.com/RECETOX/rcx-tk/actions/workflows/build.yml) |
| Citation data consistency | [](https://github.com/RECETOX/rcx-tk/actions/workflows/cffconvert.yml) |
| SonarCloud | [](https://github.com/RECETOX/rcx-tk/actions/workflows/sonarcloud.yml) |
| MarkDown link checker | [](https://github.com/RECETOX/rcx-tk/actions/workflows/markdown-link-check.yml) |
## How to use rcx_tk
`rcx-tk` package provides tools to process the metadata or alkane files.
On the input, the user is expected to supply a path to the metadata/alkane file in tsv/csv/xls/xlsx file. The file is then converted to a dataframe which is further processed. The main steps are:
- columns rearrangement
- validation of the file names
- validation that the `injectionNumber` column is of integer type
- derivation of new metadata: `sampleName`, `sequenceIdentifier`, `sampleIdentifier` and `localOrder`
Finally, the processed dataframe is saved into user-defined location.
## Installation
To install rcx_tk from GitHub repository, do:
```console
git clone git@github.com:RECETOX/rcx-tk.git
cd rcx-tk
poetry install
```
The main functions are process_metadata_file and process_alkane_ri_file.
The tool can be run also using command-line interface, either by the python3 or poetry:
```console
python3 <path-to-__main.py__> --method='' <path-to-input-data> <path-to-output-data>
```
```console
poetry run rcx_tk --method='' <file-path-to-input-data> <file-path-to-output-data>
```
## Documentation
The project is documented [here](https://rcx-tk.readthedocs.io/en/latest/?badge=latest).
## Contributing
If you want to contribute to the development of rcx_tk,
have a look at the [contribution guidelines](CONTRIBUTING.md).
## Credits
This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [NLeSC/python-template](https://github.com/NLeSC/python-template).
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