R/rc.run.msfinder.R

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

# rc.run.msfinder <- function(
#   msfinder.dir = "C:/MSFinder/msfinder",
#   input.dir  =  "R:/RSTOR-PMF/Temp/mat",
#   param.file = "R:/RSTOR-PMF/Software/MSFinder/MSFINDER.INI"
# ) {
#   
#   if(substring(msfinder.dir, nchar(msfinder.dir)) != "/") {
#     msfinder.dir <- paste0(msfinder.dir, "/")
#   }
#   
#   if(substring(input.dir, nchar(input.dir)) != "/") {
#     input.dir <- paste0(input.dir, "/")
#   }
#   
#   
#   #  MsfinderConsoleApp.exe mssearch -i .\Data\ -o .\ -m .\MsfinderConsoleApp-Param.txt
#   system(
#     paste0(
#       msfinder.dir, "MsfinderConsoleApp",
#       " mssearch ",
#       " -i ", input.dir, 
#       " -o ", input.dir, 
#       " -m ", param.file
#     )
#   )
#   
#   system(
#     paste0(
#       msfinder.dir, "MsfinderConsoleApp",
#       " predict ", 
#       " -i ", input.dir, 
#       " -o ", input.dir,
#       " -m ", param.file
#     )
#   )
#   
# }