diff topn.R @ 0:6a2bb42acfe4 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/topn.R	Tue Mar 27 06:53:36 2018 -0400
@@ -0,0 +1,88 @@
+library(XCMSwrapper)
+library(optparse)
+
+
+option_list <- list(
+  make_option("--sample_metadata", type="character"),
+  make_option("--out_dir", type="character"),
+  make_option("--class", type="character"),
+  make_option("--file_include", type="character"),
+  make_option("--cores", type="character"),
+  make_option("--scan_dens", type="numeric"),
+  make_option("--n", type="numeric"),
+  make_option("--ppm", type="numeric"),
+  make_option("--snthr", type="numeric"),
+  make_option("--minfrac", type="numeric"),
+  make_option("--polarity", type="character"),
+  make_option("--time_window_choice", type="character"),
+  make_option("--files", type="character"),
+  make_option("--galaxy_files", type="character")
+
+)
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+
+
+time_window_choice<- trimws(strsplit(opt$time_window_choice, ';')[[1]])
+time_window_choice <- time_window_choice[time_window_choice != ""]
+tdf <- plyr::ldply(time_window_choice, function(x){trimws(strsplit(x, ',')[[1]])})
+colnames(tdf) <- c('min', 'max')
+tdf$min <- as.numeric(tdf$min)
+tdf$max <- as.numeric(tdf$max)
+
+# Nearline processing
+params <- list(
+  topn.class = opt$class,
+  topn.class.files = opt$file_include,
+  topn.msPurity = TRUE,
+  topn.cores = opt$cores,
+  topn.scanDens = opt$scan_dens, # for scan range x to y, take every 'n' scan (i.e. x, x+n, x+2n ... y)
+  topn.timeRange = tdf,
+  topn.chunks = NULL, #list(c = 3, timeWin = c(0,1800)), # e.g. list(c = 3, timeWin = c(0,1800)) #chunk time range 0-1800 in to 3.
+  topn.n = opt$n, # number of peaks to take per window
+  topn.ppm = opt$ppm,
+  topn.snthr = opt$snthr,
+  topn.minfrac= opt$minfrac,
+  topn.clustType = 'hc',
+  topn.camera_xcms = '',
+  faahKO=FALSE
+)
+
+
+#
+sample_metadata <- read.table(opt$sample_metadata, sep='\t', stringsAsFactors=FALSE)
+
+filepaths <- trimws(strsplit(opt$files, ',')[[1]])
+filepaths <- filepaths[filepaths != ""]
+filepaths_wo_suffix <- unlist(lapply(filepaths, function(x){tools::file_path_sans_ext(basename(x))}))
+
+galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]])
+galaxy_files <- galaxy_files[galaxy_files != ""]
+
+if(!is.null(opt$class)){
+  # print(sample_metadata[,1])
+  file_select <- sample_metadata[,1][sample_metadata[,2]==opt$class]
+  chosen_files <- galaxy_files[filepaths_wo_suffix %in% file_select]
+}else{
+  chosen_files <- galaxy_files
+}
+print(chosen_files)
+
+if(!is.null(opt$file_include)){
+  file_include <- trimws(strsplit(opt$file_include, ',')[[1]])
+  file_include <- as.numeric(file_include[file_include != ""])
+  print(file_include)
+  chosen_files <- chosen_files[file_include]
+}
+print(chosen_files)
+params$topn.filenames = chosen_files
+
+topn = getTopn(obj=NULL, params)
+colnames(topn) = c('mzmed', 'rtmin', 'rtmax')
+topn = create_incl(grps = topn, incl_in = NULL, write_file = F, posneg = opt$polarity, comments='topn')
+
+
+print('HEAD ROWS OF TOPN')
+print(head(topn))
+write.table(topn, file.path(opt$out_dir, 'topn_peaklist.tsv'), row.names=FALSE, sep='\t')
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