--- a/frag4feature.R	Tue Feb 08 14:04:07 2022 +0000
+++ b/frag4feature.R	Wed Jun 12 16:08:23 2024 +0000
@@ -3,64 +3,61 @@
 library(xcms)
 print(sessionInfo())
 
-xset_pa_filename_fix <- function(opt, pa, xset=NULL) {
-
+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
 
-  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 <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint
+        filepaths <- filepaths[filepaths != ""]
 
-    filepaths <- filepaths[filepaths != ""]
-
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
-    galaxy_names <- galaxy_names[galaxy_names != ""]
+        galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
+        galaxy_names <- galaxy_names[galaxy_names != ""]
 
-    nsave <- names(pa@fileList)
-    old_filenames  <- basename(pa@fileList)
+        nsave <- names(pa@fileList)
+        old_filenames <- basename(pa@fileList)
 
-    pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
-    names(pa@fileList) <- nsave
+        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)
+        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 (!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)
-       }
-   }
- }
+        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))
+    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")
+    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
@@ -68,17 +65,18 @@
 print(opt)
 
 loadRData <- function(rdata_path, name) {
-#loads an RData file, and returns the named xset object if it is there
+    # 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
+# @author Gildas Le Corguille lecorguille@sb-roscoff.fr
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
-    if (class(xobject) == "xcmsSet")
+    if (class(xobject) == "xcmsSet") {
         return(xobject)
+    }
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
@@ -99,20 +97,20 @@
 print(xset@filepaths)
 
 if (is.null(opt$intense)) {
-  intense <- FALSE
-}else{
-  intense <- TRUE
+    intense <- FALSE
+} else {
+    intense <- TRUE
 }
 
 if (is.null(opt$convert2RawRT)) {
     convert2RawRT <- FALSE
-}else{
+} else {
     convert2RawRT <- TRUE
 }
 
 if (is.null(opt$createDB)) {
     createDB <- FALSE
-}else{
+} else {
     createDB <- TRUE
 }
 
@@ -121,7 +119,7 @@
     pa <- fix[[1]]
     xset <- fix[[2]]
     useGroup <- FALSE
-}else{
+} 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)
@@ -132,22 +130,24 @@
 
 if (is.null(opt$grp_peaklist)) {
     grp_peaklist <- NA
-}else{
+} else {
     grp_peaklist <- opt$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$out_dir,
-                             grp_peaklist = grp_peaklist,
-                             create_db = createDB,
-                             use_group = useGroup)
+pa <- msPurity::frag4feature(
+    pa = pa,
+    xset = xset,
+    ppm = opt$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"))