Scripting
LEAF targeted analyses can be run without the web UI in two ways:
| Task | Interface |
|---|---|
| Drive analyses from a terminal — schedule, batch, integrate with shell pipelines | The leaf command-line interface |
| Embed LEAF in Python pipelines (Snakemake, Nextflow, custom scripts, notebooks) | The leaf Python package |
Both interfaces operate on the same targeted result format as the web UI: a .msd produced by the UI loads in a script, and vice versa.
When to script vs use the UI
| Web UI recommended for | Scripted interface recommended for |
|---|---|
| Performing exploratory or interactive analysis | Running batch analyses on many datasets with shared parameters |
| Reviewing peak quality and adjusting integrations manually | Reproducing an analysis as part of a manuscript or pipeline |
| Producing visualizations for inspection | Integrating LEAF results with downstream Python tools (pandas, scikit-learn, etc.) |
| One-off or ad hoc work | Embedding LEAF in a multi-step workflow |
Where to start
leaf webui— start the web UI from a terminal (most common)leaf targeted— targeted extraction headlessleaf watch— auto-extract new LC-MS files as they land in a folder- Python recipes — common scripted-analysis tasks
- SEED — the Rust reader powering LEAF on macOS / Linux