CLI Usage

The WTV CLI provides an easy way to perform ion selection on mass spectrometry data.

Basic Command

wtv-cli --msp_path input.msp --outpath output --mz_min 35 --mz_max 400 ...

When using uv:

uv run wtv-cli --msp_path input.msp --outpath output ...

Options

Option	Description	Default
--msp_path	Path to the input MSP file.	Required
--outpath	Directory to save the output files.	Required
--mz_min	Minimum m/z value.	35
--mz_max	Maximum m/z value.	400
--rt_window	Retention time window.	2.00
--min_ion_intensity_percent	Minimum ion intensity percentage.	7
--min_ion_num	Minimum number of ions.	2
--prefer_mz_threshold	Preferred m/z threshold.	60
--similarity_threshold	Similarity threshold.	0.85
--fr_factor	FR factor.	2.0
--retention_time_max	Maximum retention time.	68.80

Examples

Basic Usage

Run ion selection with default parameters:

wtv-cli \
    --msp_path input.msp \
    --outpath ./output \
    --mz_min 35 \
    --mz_max 400 \
    --rt_window 2.0 \
    --min_ion_intensity_percent 7 \
    --min_ion_num 2 \
    --prefer_mz_threshold 60 \
    --similarity_threshold 0.85 \
    --fr_factor 2.0 \
    --retention_time_max 68.80

Custom Parameters

Adjust parameters for your specific data:

wtv-cli \
    --msp_path my_data.msp \
    --outpath ./results \
    --mz_min 50 \
    --mz_max 500 \
    --rt_window 1.5 \
    --similarity_threshold 0.9

Using with uv

If you installed with uv, run:

uv run wtv-cli --msp_path input.msp --outpath ./output --mz_min 35 --mz_max 400

Output

The CLI generates an MSP file in the specified output directory containing the filtered spectra based on the ion selection algorithm.