R/sirius.command.line.R

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

# system(
#   paste0(
#     "/home/pmflab/sirius-gui/bin/sirius ", 
#     "-i=",
#     "/home/pmflab/RStor/Projects/20210701-KWEBB-KW-1044/TOF_T3_Pos/spectra/ms", 
#     " -o=",
#     "/home/pmflab/RStor/Projects/20210701-KWEBB-KW-1044/TOF_T3_Pos/spectra/ms/out",
#     " --recompute ", 
#     "--naming-convention=%compoundname ", 
#     "--cores 24 ",
#     # "--compound-timeout=20 ", 
#     "formula ",
#     "-d ", 
#     "bio ", 
#     "-p ", 
#     "qtof ", 
#     "zodiac ", 
#     "structure ", 
#     "canopus"
#   )
# )
#