R/rc.run.msfinder.mssearch.R

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

# rc.run.sirius <- function(
#   sirius.dir = "/home/pmflab/sirius-gui/bin/sirius",
#   input.dir  =  "/home/pmflab/RStor/Projects/20210701-KWEBB-KW-1044/TOF_T3_Pos/spectra/ms",
#   output.dir = "out"
# ) {
#   
#   system(
#     paste0(
#       sirius.dir, " ",
#       "-i=",
#       input.dir, 
#       " -o=",
#       input.dir, "/out",
#       " --recompute ", 
#       "--naming-convention=%compoundname ", 
#       "--cores 24 ",
#       "formula ",
#       "-d ", 
#       "bio ", 
#       "-p ", 
#       "qtof ", 
#       "zodiac ", 
#       "structure ", 
#       "canopus"
#     )
#   )
#   
# }
#