--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/frag4feature.R	Thu Mar 04 12:11:29 2021 +0000
@@ -0,0 +1,157 @@
+library(optparse)
+library(msPurity)
+library(xcms)
+print(sessionInfo())
+
+xset_pa_filename_fix <- function(opt, pa, xset=NULL) {
+
+
+  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$mzML_files, ",")[[1]]) # nolint
+
+    filepaths <- filepaths[filepaths != ""]
+
+    galaxy_names <- trimws(strsplit(opt$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)])
+  }
+  print(pa@fileList)
+
+  if (!is.null(xset)) {
+
+    print(xset@filepaths)
+
+    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)
+       }
+   }
+ }
+
+  return(list(pa, xset))
+}
+
+
+option_list <- list(
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option("--pa", type = "character"),
+  make_option("--xset", type = "character"),
+  make_option("--ppm", default = 10),
+  make_option("--plim", default = 0.0),
+  make_option("--convert2RawRT", action = "store_true"),
+  make_option("--intense", action = "store_true"),
+  make_option("--createDB", action = "store_true"),
+  make_option("--cores", default = 4),
+  make_option("--mzML_files", type = "character"),
+  make_option("--galaxy_names", type = "character"),
+  make_option("--grp_peaklist", type = "character"),
+  make_option("--useGroup", action = "store_true")
+)
+
+# 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]))
+}
+
+# This function retrieve a xset like object
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
+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"))
+        sampclass(xset) <- xset@phenoData$sample_group
+        return(xset)
+    }
+}
+
+# Requires
+pa <- loadRData(opt$pa, "pa")
+xset <- loadRData(opt$xset, c("xset", "xdata"))
+xset <- getxcmsSetObject(xset)
+
+pa@cores <- opt$cores
+
+print(pa@fileList)
+print(xset@filepaths)
+
+if (is.null(opt$intense)) {
+  intense <- FALSE
+}else{
+  intense <- TRUE
+}
+
+if (is.null(opt$convert2RawRT)) {
+    convert2RawRT <- FALSE
+}else{
+    convert2RawRT <- TRUE
+}
+
+if (is.null(opt$createDB)) {
+    createDB <- FALSE
+}else{
+    createDB <- TRUE
+}
+
+if (is.null(opt$useGroup)) {
+    fix <- xset_pa_filename_fix(opt, pa, xset)
+    pa <- fix[[1]]
+    xset <- fix[[2]]
+    useGroup <- FALSE
+}else{
+    # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
+    print("useGroup")
+    fix <- xset_pa_filename_fix(opt, pa)
+    pa <- fix[[1]]
+    useGroup <- TRUE
+}
+
+
+if (is.null(opt$grp_peaklist)) {
+    grp_peaklist <- NA
+}else{
+    grp_peaklist <- opt$grp_peaklist
+}
+print(useGroup)
+
+pa <- msPurity::frag4feature(pa = pa,
+                             xset = xset,
+                             ppm = opt$ppm,
+                             plim = opt$plim,
+                             intense = intense,
+                             convert2RawRT = convert2RawRT,
+                             db_name = "alldata.sqlite",
+                             out_dir = opt$out_dir,
+                             grp_peaklist = grp_peaklist,
+                             create_db = createDB,
+                             use_group = useGroup)
+print(pa)
+save(pa, file = file.path(opt$out_dir, "frag4feature_output.RData"))
+
+pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
+
+print(head(pa@grped_df))
+write.table(pa@grped_df, file.path(opt$out_dir, "frag4feature_output.tsv"), row.names = FALSE, sep = "\t")