#' @title findpwiz
#' @export
#' @rdname findpwiz
#' @param userGivenPath directory that contains "Specify_ProteoWizard_Location.txt"
#' @param proteoWizardLocation directory that contains msconvert.exe
#' @return filepath of the folder containing msconvert.exe
findpwiz <- function(userGivenPath, proteoWizardLocation){
msconvertLocation <- list.files(proteoWizardLocation, recursive = TRUE, pattern = "msconvert.exe", full.names = TRUE)
if(length(msconvertLocation) >= 1){ # If length is 1 or greater then msconvert.exe was found (or multiple installations), return one
msconvertLocation <- dirname(msconvertLocation[[1]])
}
# Check if msconvert was found. If not, look for path provided by user.
if(length(msconvertLocation) == 0){
msconvertLocation <- readLines(file.path(userGivenPath,"Specify_ProteoWizard_Location.txt"))
if (length(msconvertLocation) == 0){ # Empty file check
msconvertLocation <- "Unable to find msconvert.exe in \"Program Files\" and no location provided in: <br> mzEasy\\www\\Specify_ProteoWizard_Location.txt"
}else{
# Ensure consistent "/" "\"
msconvertLocation <- gsub("\\\\\\\\", "\\\\", msconvertLocation)
msconvertLocation <- gsub("/", "\\\\", msconvertLocation)
if(dir.exists(msconvertLocation)){
msconvertLocation <- list.files(msconvertLocation, recursive = TRUE, pattern = "msconvert.exe", full.names = TRUE)
if(length(msconvertLocation) >= 1){
msconvertLocation <- dirname(msconvertLocation[[1]])
}else{
msconvertLocation <- "Unable to find msconvert.exe in \"Program Files\" and did not find msconvert.exe within location provided in: <br> mzEasy\\www\\Specify_ProteoWizard_Location.txt"
}
}else{
msconvertLocation <- "Unable to find msconvert.exe in \"Program Files\" and did not find msconvert.exe within location provided in: <br> mzEasy\\www\\Specify_ProteoWizard_Location.txt"
}
}
}
return(msconvertLocation)
}
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