Command-Line Interface

The leaf command-line interface ships with the LEAF Python package. This manual documents the targeted analysis commands, service commands, and setup / file utilities:

Sub-command	Purpose	Reference
leaf webui	Start / stop the local web application (run, start, stop, status)	Detail
leaf targeted	Targeted metabolite extraction, peak picking, and quality scoring (no UI)	Detail
leaf watch	Real-time folder monitoring; auto-extracts new LC-MS files (run, start, stop, status)	Detail
leaf doctor	Check the local Python package, native extensions, reader support, and Web UI assets	Detail
leaf validate	Preflight a metabolite list and optional RAW / mzML input path	Detail
leaf init	Create a starter analysis folder	Detail
leaf inspect	Summarize saved .msd result archives and acquisition files	Detail
leaf update	Upgrade LEAF in the active Python environment	Detail
leaf convert	Convert Thermo RAW folders to mzML	Detail

For programmatic use without a CLI, see the Python package documentation.

Verifying the installation

leaf --version
leaf doctor

Expected output:

leaf 0.5.7

If the command is not found, the install location is not on PATH. Resolutions are listed in Install the wheel + CLI — Troubleshooting.

Legacy aliases

One console-script shim preserves compatibility with existing watcher scripts:

Shim	Equivalent to
leaf-watch	leaf watch run

The CLI also accepts leaf analyze as a hidden deprecated alias for leaf targeted. New scripts should use leaf targeted.

Configuration

Persistent settings (storage paths, default backend, worker counts) are configured through the Settings dialog in the web UI. Configuration on disk is described in Configuration.

Next

→ leaf webui — start the web application → Setup & file tools — check installs, validate inputs, inspect results → Configuration — config files and environment variables