example_parameter_file.ini

[moFF_parameters]
loc_in= sample_data/
# you can comment each voice  using #
# use a space to separate each item
#tsv_list= sample_data/20080311_CPTAC6_07_6A005.txt sample_data/20080311_CPTAC6_10_6B019.txt sample_data/20080311_CPTAC6_13_6C012.txt
#raw_list = your_local_folder_raw_repo//20080311_CPTAC6_07_6A005.RAW your_local_folder_raw_repo//raw_repo/20080311_CPTAC6_10_6B019.RAW your_local_folder_raw_repo//20080311_CPTAC6_13_6C012.RAW
# folder where all the raw files are located
raw_repo= your_local_folder_raw_repo/
# lenght of XIC
xic_length= 3
# size of the rt win used to find the for  MS2 identified peptides
rt_peak_win= 1
# size of the rt win used to find the for  machted  peptides
rt_peak_win_match= 1
# tollerance in ppm
tol= 10
# export the peptide summary for further analysis True/False. to set to False left empy
peptide_summary = True
# set output folder
loc_out= output_data/
#specify witch replicated to use for mbr reg_exp are valid . i.e: *_A*.txt
sample=
# specify the file extentention of the input like
ext=txt
# a label name to use for the log file
log_label = moFF
#width value of the filter  k * mean(Dist_Malahobis) . default value 2
w_filt = 2
# filter outlier in each rt time allignment . default value True.  to set to False left empy
out_flag = True
#weigthing schema  True/False  to set to False left empy
w_comb  =
#  select the moFF workflow: on = mbr + apex , off = apex only , only= only mbr
mbr = on
# activate /deactivate the filtering.  to set to False left empy
match_filter = True
#choose the ptm json schema
ptm_file = ptm_setting_mq.json
# quantile value used to compute the filtering threshold for the matched peak
quantile_thr_filtering = 0.75
# percentage of MS2 peptide used to estimated the threshold.
sample_size = 0.20
# number of cpu. use 0 to automatically detects the cpu numbers in your machine
cpu 0