Metadata-Version: 2.4
Name: radiant-fulcrum-workflow
Version: 0.3.3
Summary: Radiant DIA workflow plugin for Fulcrum Pipeline
Home-page: https://github.com/seerbio/radiant-fulcrum-workflow
Author: Seth Just
Author-email: sjust@seer.bio
Project-URL: Bug Tracker, https://github.com/seerbio/radiant-fulcrum-workflow/issues
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: fulcrum-ms<2.0.0,>=1.1.0
Requires-Dist: wheely-radiant<2.0.0,>=0.5.0
Requires-Dist: wheely-mammoth<2.0.0,>=0.7.6
Requires-Dist: dotdict
Provides-Extra: local
Requires-Dist: radiant-fulcrum-search; extra == "local"
Provides-Extra: docs
Requires-Dist: numpydoc>=1.0.0; extra == "docs"
Requires-Dist: sphinx-argparse>=0.2.5; extra == "docs"
Requires-Dist: sphinx-rtd-theme>=0.5.0; extra == "docs"
Requires-Dist: nbsphinx>=0.7.1; extra == "docs"
Requires-Dist: ipykernel>=5.3.0; extra == "docs"
Requires-Dist: recommonmark>=0.5.0; extra == "docs"
Provides-Extra: dev
Requires-Dist: pre-commit>=2.7.1; extra == "dev"
Requires-Dist: black>=20.8b1; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Dynamic: license-file

# Radiant DIA workflow plugin for Fulcrum Pipeline

This plugin permits running Radiant DIA™ searches with straightforward configuration.
Many key choices are made for the user to simplify the experience.

## Installation  

This library requires Python 3.10+ and can be installed with pip:  

```shell
pip install 'radiant-fulcrum-workflow[local]'
```

## Basic Usage  

After [installation](#installation), you can directly run the `radiant_fulcrum` command from the terminal:

```shell
radiant_fulcrum --library /path/to/library.tsv --fasta /path/to/database.fasta --config /path/to/config.radiantConfig file1.mzML file2.mzML
```

For a full list of arguments, run:

```shell
radiant_fulcrum --help
```

## Advanced Usage in the Fulcrum Pipeline

This package provides plugins for [Fulcrum Pipeline™](https://github.com/seerbio/fulcrum/).

After [installation](#installation) you may use the
following parameters:

```toml
workflow = "radiant"
library = "/path/to/library.tsv"
fasta = "/path/to/database.fasta"
config = "/path/to/config.radiantConfig"

mzml = [
"file1.mzML",
"file2.mzML",
]
```

For a complete list of supported parameters, see the project's documentation (linked in the sidebar above).
