--- a/assess_purity_msms.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-library(msPurity)
-library(optparse)
-print(sessionInfo())
-
-option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--mzML_files", type="character"),
-  make_option("--galaxy_names", type="character"),
-  make_option("--minOffset", default=0.5),
-  make_option("--maxOffset", default=0.5),
-  make_option("--ilim", default=0.05),
-  make_option("--iwNorm", default="none", type="character"),
-  make_option("--exclude_isotopes", action="store_true"),
-  make_option("--isotope_matrix", type="character"),
-  make_option("--mostIntense", action="store_true"),
-  make_option("--plotP", action="store_true"),
-  make_option("--nearest", action="store_true"),
-  make_option("--cores", default=4)
-)
-
-# store options
-opt<- parse_args(OptionParser(option_list=option_list))
-
-minOffset = as.numeric(opt$minOffset)
-maxOffset = as.numeric(opt$maxOffset)
-
-if (opt$iwNorm=='none'){
-    iwNorm = FALSE
-    iwNormFun = NULL
-}else if (opt$iwNorm=='gauss'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='rcosine'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='QE5'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormQE.5()
-}
-
-filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
-filepaths <- filepaths[filepaths != ""]
-
-
-
-if(is.null(opt$minOffset) || is.null(opt$maxOffset)){
-    offsets = NA
-}else{
-    offsets = as.numeric(c(opt$minOffset, opt$maxOffset))
-}
-
-
-if(is.null(opt$mostIntense)){
-    mostIntense = FALSE
-}else{
-    mostIntense = TRUE
-}
-
-if(is.null(opt$nearest)){
-    nearest = FALSE
-}else{
-    nearest = TRUE
-}
-
-if(is.null(opt$plotP)){
-    plotP = FALSE
-    plotdir = NULL
-}else{
-    plotP = TRUE
-    plotdir = opt$out_dir
-}
-
-
-if (is.null(opt$isotope_matrix)){
-    im <- NULL
-}else{
-    im <- read.table(opt$isotope_matrix,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
-}
-
-if (is.null(opt$exclude_isotopes)){
-    isotopes <- FALSE
-}else{
-    isotopes <- TRUE
-}
-
-pa <- msPurity::purityA(filepaths,
-                        cores = opt$cores,
-                        mostIntense = mostIntense,
-                        nearest = nearest,
-                        offsets = offsets,
-                        plotP = plotP,
-                        plotdir = plotdir,
-                        interpol = "linear",
-                        iwNorm = iwNorm,
-                        iwNormFun = iwNormFun,
-                        ilim = opt$ilim,
-                        mzRback = "pwiz",
-                        isotopes = isotopes,
-                        im = im)
-
-
-if (!is.null(opt$galaxy_names)){
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
-    galaxy_names <- galaxy_names[galaxy_names != ""]
-    names(pa@fileList) <- galaxy_names
-}
-
-print(pa)
-
-save(pa, file=file.path(opt$out_dir, 'purity_msms.RData'))
-
-print(head(pa@puritydf))
-write.table(pa@puritydf, file.path(opt$out_dir, 'purity_msms.tsv'), row.names=FALSE, sep='\t')
-
-# removed_peaks <- data.frame(removed_peaks)
-# write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
-#         file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')