diff lcms-interval-scheduling.R @ 1:defa57c7775e draft

planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms-interval-scheduling.R	Tue Mar 27 07:18:42 2018 -0400
@@ -0,0 +1,109 @@
+library(XCMSwrapper)
+library(optparse)
+
+option_list <- list(
+
+  make_option(c("-s", "--sample_peaklist"), type="character"),
+  make_option(c("-b", "--blank_peaklist"), type="character"),
+  make_option(c("-t", "--topn"), type="character"),
+  make_option(c("-o", "--out_dir"), type="character", default=getwd(),
+              help="Output folder for resulting files [default = %default]"
+  ),
+  make_option("--method", type="character"),
+  make_option("--maxms2", type="numeric"),
+  make_option("--widthFactor", type="numeric"),
+  make_option("--minWidth", type="numeric"),
+  make_option("--ilimit", type="numeric"),
+  make_option("--shift", type="numeric"),
+  make_option("--samplelistNm", type="numeric"),
+  make_option("--overlappingP", type="numeric"),
+  make_option("--fullpw", action="store_true"),
+  make_option("--b_widthFactor", type="numeric"),
+  make_option("--b_shift", type="numeric"),
+  make_option("--b_exclu_limit", type="numeric"),
+  make_option("--b_minWidth", type="numeric"),
+  make_option("--polarity", type="character"),
+  make_option("--fillgaps", type="character"),
+  make_option("--dmaNearline", action="store_true"),
+  make_option("--blankClass", type="character"),
+  make_option("--intensityCN", type="character"),
+  make_option("--sortCN", type="character"),
+  make_option("--filterS", type="character")
+)
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+
+print(sessionInfo())
+print(opt)
+
+if(is.null(opt$fullpw)){
+  fullpw = FALSE
+}else{
+  fullpw = TRUE
+}
+
+if(is.null(opt$fillgaps)){
+  fillgaps = FALSE
+}else{
+  fillgaps = TRUE
+}
+
+
+# Nearline processing
+# nearline parameters (sample and blank)
+params <- list(
+  nl.method = opt$method,
+  nl.maxms2 = opt$maxms2, # only used for simple nearline
+  nl.widthFactor = opt$widthFactor,
+  nl.minWidth = opt$minWidth, # 5 seconds
+  nl.ilimit = opt$ilimit, # only used for simple nearline
+  nl.shift = opt$shift,
+  nl.samplelist_nm  = opt$samplelistNm,
+  nl.overlappingP  = opt$overlappingP,
+  nl.fullpw = fullpw,
+  nl.fillgaps = fillgaps,  # only used for metshot nearline
+  #nearline blank parameters
+  nl.b_widthFactor = opt$b_widthFactor, # increase the width
+  nl.b_minWidth = opt$b_minWidth,
+  nl.b.shift = opt$b_shift,
+  nl.exclu_limit = opt$b_exclu_limit,
+  temp_dir='.',
+  intensityCN=opt$intensityCN,
+  sortCN=opt$sortCN # column of the sample peaklist to use for
+
+)
+
+
+
+# ##################################
+# # Perform Nearline optimisation
+# ##################################
+s_peaklist <- read.table(opt$sample_peaklist, header = TRUE, sep='\t', stringsAsFactors = FALSE)
+b_peaklist <- read.table(opt$blank_peaklist, header = TRUE, sep='\t', stringsAsFactors = FALSE)
+
+if(!is.null(opt$dmaNearline)){
+    # have to do some additional filtering if part of the dma nearline workflow
+    blank_class_name <- gsub('-', '.', opt$blankClass)
+    b_peaklist = b_peaklist[which(b_peaklist[,paste(blank_class_name, '_valid', sep='')]==1),]
+    s_peaklist = s_peaklist[s_peaklist[,opt$filterS]==0,]
+}
+
+
+
+topn <- read.table(opt$topn, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names=FALSE)
+topn[is.na(topn)] <- ""
+# colnames(topn) <- c('Mass [m/z]', 'Formula [M]', 'Formula type', 'Species',   'CS [z]',  'Polarity',  'Start [min]',  'End [min]','Comment')
+# colnames(topn) <- gsub('\\.', ' ', colnames(topn))
+print(head(topn))
+
+# #Generate inclusions lists for DDA-MS/MS and store in list
+incl.lists = nearline_main(pm = params, peaklist_xcms=s_peaklist, pol=opt$polarity, merge_peaklists=FALSE, peaklist_post=NA)
+
+# #Generate exclusion lists for each class being analysed
+nearline_main_blank(pm = params,
+                        plist = b_peaklist,
+                        incl_list_pos = incl.lists,
+                        pol = opt$polarity,
+                        topn = topn)
+#