From msconvert_parameter class to running code
from_msconvert_parameter_to_code(msconvert_parameter)msconvert_parameter class object.
Running code for docker.
parameter1 =
create_msconvert_parameter(
output_format = "mzXML",
binary_encoding_precision = "64",
zlib = TRUE,
write_index = TRUE,
peak_picking_algorithm = "vendor",
vendor_mslevels = c(1, 2),
cwt_mslevels = c(1, NA),
cwt_min_snr = 0.1,
cwt_min_peak_spacing = 0.1,
subset_polarity = "any",
subset_scan_number = c(NA, NA),
subset_scan_time = c(NA, NA),
subset_mslevels = c(1, NA),
zero_samples_mode = "no",
zero_samples_mslevels = c(1, NA),
zero_samples_add_missing_flanking_zero_count = 5
)
from_msconvert_parameter_to_code(parameter1)
#> [1] "--mzXML --64 --zlib --filter \"peakPicking vendor msLevel=1-2\" --filter \"msLevel 1-\""
parameter2 =
create_msconvert_parameter(
output_format = "mzXML",
binary_encoding_precision = "32",
zlib = TRUE,
write_index = TRUE,
peak_picking_algorithm = "cwt",
vendor_mslevels = c(1, NA),
cwt_mslevels = c(1, NA),
cwt_min_snr = 0.1,
cwt_min_peak_spacing = 0.1,
subset_polarity = "positive",
subset_scan_number = c(NA, NA),
subset_scan_time = c(60, 300),
subset_mslevels = c(1, 2),
zero_samples_mode = "removeExtra",
zero_samples_mslevels = c(1, NA),
zero_samples_add_missing_flanking_zero_count = 5
)
parameter2
#> --------------------
#> pacakge_name: massconverter
#> function_name: create_msconvert_parameter
#> time: 2022-09-19 16:18:57
#> parameters:
#> output_format : mzXML
#> binary_encoding_precision : 32
#> zlib : TRUE
#> write_index : TRUE
#> peak_picking_algorithm : cwt
#> vendor_mslevels : c(1, NA)
#> cwt_mslevels : c(1, NA)
#> cwt_min_snr : 0.1
#> cwt_min_peak_spacing : 0.1
#> subset_polarity : positive
#> subset_scan_number : c(NA, NA)
#> subset_scan_time : c(60, 300)
#> subset_mslevels : c(1, 2)
#> zero_samples_mode : removeExtra
#> zero_samples_mslevels : c(1, NA)
#> zero_samples_add_missing_flanking_zero_count : 5
from_msconvert_parameter_to_code(parameter2)
#> [1] "--mzXML --32 --zlib --filter \"peakPicking cwt snr=0.1 peakSpace=0.1 msLevel=1-\" --filter \"polarity positive\" --filter \"scanTime [60,300]\" --filter \"msLevel 1-2\" --filter \"zeroSamples removeExtra 1-\""