--- a/frag4feature.R	Fri Nov 13 09:47:47 2020 +0000
+++ b/frag4feature.R	Thu Mar 04 12:25:25 2021 +0000
@@ -3,18 +3,18 @@
 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)){
+  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$mzML_files, ',')[[1]])
+    filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint
+
     filepaths <- filepaths[filepaths != ""]
-    new_names <- basename(filepaths)
 
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
     galaxy_names <- galaxy_names[galaxy_names != ""]
 
     nsave <- names(pa@fileList)
@@ -28,14 +28,14 @@
   }
   print(pa@fileList)
 
-  if(!is.null(xset)){
+  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')
+    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)
@@ -48,26 +48,26 @@
 
 
 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
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
-loadRData <- function(rdata_path, name){
+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]))
@@ -78,19 +78,19 @@
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
     if (class(xobject) == "xcmsSet")
-        return (xobject)
+        return(xobject)
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
         sampclass(xset) <- xset@phenoData$sample_group
-        return (xset)
+        return(xset)
     }
 }
 
 # Requires
-pa <- loadRData(opt$pa, 'pa')
-xset <- loadRData(opt$xset, c('xset','xdata'))
+pa <- loadRData(opt$pa, "pa")
+xset <- loadRData(opt$xset, c("xset", "xdata"))
 xset <- getxcmsSetObject(xset)
 
 pa@cores <- opt$cores
@@ -98,63 +98,60 @@
 print(pa@fileList)
 print(xset@filepaths)
 
-if(is.null(opt$intense)){
-  intense = FALSE
+if (is.null(opt$intense)) {
+  intense <- FALSE
 }else{
-  intense = TRUE
+  intense <- TRUE
 }
 
-if(is.null(opt$convert2RawRT)){
-    convert2RawRT = FALSE
+if (is.null(opt$convert2RawRT)) {
+    convert2RawRT <- FALSE
 }else{
-    convert2RawRT= TRUE
+    convert2RawRT <- TRUE
 }
 
-if(is.null(opt$createDB)){
-    createDB = FALSE
+if (is.null(opt$createDB)) {
+    createDB <- FALSE
 }else{
-    createDB = TRUE
+    createDB <- TRUE
 }
 
-if(is.null(opt$useGroup)){
+if (is.null(opt$useGroup)) {
     fix <- xset_pa_filename_fix(opt, pa, xset)
     pa <- fix[[1]]
     xset <- fix[[2]]
-    useGroup=FALSE
+    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')
+    print("useGroup")
     fix <- xset_pa_filename_fix(opt, pa)
     pa <- fix[[1]]
-    useGroup=TRUE
+    useGroup <- TRUE
 }
 
 
-if(is.null(opt$grp_peaklist)){
-    grp_peaklist = NA
+if (is.null(opt$grp_peaklist)) {
+    grp_peaklist <- NA
 }else{
-    grp_peaklist = opt$grp_peaklist
+    grp_peaklist <- opt$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$out_dir, 'frag4feature_output.RData'))
+save(pa, file = file.path(opt$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$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t')
+write.table(pa@grped_df, file.path(opt$out_dir, "frag4feature_output.tsv"), row.names = FALSE, sep = "\t")