--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/createDatabase.R	Thu Mar 04 12:17:52 2021 +0000
@@ -0,0 +1,168 @@
+library(msPurity)
+library(optparse)
+library(xcms)
+library(CAMERA)
+print(sessionInfo())
+print("CREATING DATABASE")
+
+xset_pa_filename_fix <- function(opt, pa, xset) {
+
+  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
+    # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
+    # needs to be done due to Galaxy moving the files around and screwing up any links to files
+
+    filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
+    filepaths <- filepaths[filepaths != ""]
+
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
+    galaxy_names <- galaxy_names[galaxy_names != ""]
+
+    nsave <- names(pa@fileList)
+    old_filenames  <- basename(pa@fileList)
+    pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
+    names(pa@fileList) <- nsave
+
+    pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
+    pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
+  }
+
+
+ if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
+    if (!all(names(pa@fileList) == basename(xset@filepaths))) {
+       print("FILELISTS DO NOT MATCH")
+       message("FILELISTS DO NOT MATCH")
+       quit(status = 1)
+    }else{
+      xset@filepaths <- unname(pa@fileList)
+    }
+  }
+
+  print(xset@phenoData)
+  print(xset@filepaths)
+
+  return(list(pa, xset))
+}
+
+
+
+
+option_list <- list(
+  make_option(c("-o", "--outDir"), type = "character"),
+  make_option("--pa", type = "character"),
+  make_option("--xset_xa", type = "character"),
+  make_option("--xcms_camera_option", type = "character"),
+  make_option("--eic", action = "store_true"),
+  make_option("--cores", default = 4),
+  make_option("--mzML_files", type = "character"),
+  make_option("--galaxy_names", type = "character"),
+  make_option("--grpPeaklist", type = "character")
+)
+
+
+# store options
+opt <- parse_args(OptionParser(option_list = option_list))
+print(opt)
+
+loadRData <- function(rdata_path, name) {
+#loads an RData file, and returns the named xset object if it is there
+    load(rdata_path)
+    return(get(ls()[ls() %in% name]))
+}
+
+getxcmsSetObject <- function(xobject) {
+    # XCMS 1.x
+    if (class(xobject) == "xcmsSet")
+        return(xobject)
+    # XCMS 3.x
+    if (class(xobject) == "XCMSnExp") {
+        # Get the legacy xcmsSet object
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
+        xcms::sampclass(xset) <- xset@phenoData$sample_group
+        return(xset)
+    }
+}
+
+
+print(paste("pa", opt$pa))
+print(opt$xset)
+
+print(opt$xcms_camera_option)
+# Requires
+pa <- loadRData(opt$pa, "pa")
+
+
+print(pa@fileList)
+
+# Missing list element causes failures (should be updated
+# in msPurity R package for future releases)
+if (!exists("allfrag", where = pa@filter_frag_params)) {
+    pa@filter_frag_params$allfrag <- FALSE
+}
+
+if (opt$xcms_camera_option == "xcms") {
+
+  xset <- loadRData(opt$xset, c("xset", "xdata"))
+  xset <- getxcmsSetObject(xset)
+  fix <- xset_pa_filename_fix(opt, pa, xset)
+  pa <- fix[[1]]
+  xset <- fix[[2]]
+  xa <- NULL
+}else{
+
+  xa <- loadRData(opt$xset, "xa")
+  fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
+  pa <- fix[[1]]
+  xa@xcmsSet <- fix[[2]]
+  xset <- NULL
+}
+
+
+if (is.null(opt$grpPeaklist)) {
+  grpPeaklist <- NA
+}else{
+  grpPeaklist <- opt$grpPeaklist
+}
+
+dbPth <- msPurity::createDatabase(pa,
+                                   xset = xset,
+                                   xsa = xa,
+                                   outDir = opt$outDir,
+                                   grpPeaklist = grpPeaklist,
+                                   dbName = "createDatabase_output.sqlite"
+)
+
+
+
+
+
+if (!is.null(opt$eic)) {
+
+  if (is.null(xset)) {
+      xset <- xa@xcmsSet
+  }
+  # previous check should have matched filelists together
+  xset@filepaths <- unname(pa@fileList)
+
+  convert2Raw <- function(x, xset) {
+    sid <- unique(x$sample)
+    # for each file get list of peaks
+    x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
+    x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
+    x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
+    return(x)
+
+  }
+
+  xset@peaks <- as.matrix(
+    plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset = xset))
+
+  # Saves the EICS into the previously created database
+  px <- msPurity::purityX(xset,
+                          saveEIC = TRUE,
+                          cores = 1,
+                          sqlitePth = dbPth,
+                          rtrawColumns = TRUE)
+
+}
+
+closeAllConnections()