--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/frag4feature.R	Wed Nov 27 13:35:22 2019 -0500
@@ -0,0 +1,160 @@
+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$mzML_files, ',')[[1]])
+    filepaths <- filepaths[filepaths != ""]
+    new_names <- basename(filepaths)
+
+    galaxy_names <- trimws(strsplit(opt$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')