[experiment]
controller_name	= SmartROI
min_rt = 0
max_rt = 1440
ionisation_mode = Positive
isolation_width = 1

[roi_extraction]
mz_tol = 5
mz_units = ppm
min_length = 1
min_intensity = 0
	
[simulation]
N = 10
mz_tol = 10
rt_tol = 15
min_ms1_intensity = 5000
iif_values = [2, 3, 5, 10, 1e3, 1e6]
dp_values = [0, 0.1, 0.5, 1, 5]
min_roi_intensity = 500
min_roi_length = 0
min_roi_length_for_fragmentation = 0

# leave blank to compute timing from the seed data itself
time_dict = 

# TODO: should be removed eventually
ps_file = /Users/joewa/University of Glasgow/Vinny Davies - CLDS Metabolomics Project/Trained Models/peak_sampler_mz_rt_int_beerqcb_fragmentation.p 

[evaluation]
mzmine_command = /Users/joewa/work/MZmine-2.40.1/startMZmine_Windows.bat
mzmine_xml_file = /Users/joewa/Work/git/vimms/batch_files/QC_PP.xml

