--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/decon.R	Wed Aug 06 08:38:24 2025 +0000
@@ -0,0 +1,79 @@
+suppressPackageStartupMessages(library(microDecon))
+suppressPackageStartupMessages(library(optparse))
+
+# Define command-line options
+option_list <- list(
+    make_option(c("-m", "--mode"), type = "character", help = "Mode of operation: decon, remove.cont, remove.thresh, decon.diff", metavar = "MODE"),
+    make_option(c("-d", "--data_file"), type = "character", help = "Path to the data file (CSV format expected)", metavar = "FILE"),
+    make_option(c("-o", "--output"), type = "character", default = NULL, help = "Output file from remove.cont or remove.thresh (used in decon.diff)", metavar = "FILE"),
+    make_option(c("-b", "--numb_blanks"), type = "integer", default = NULL, help = "Number of blank samples"),
+    make_option(c("-n", "--numb_ind"), type = "character", default = NULL, help = "Number of individuals (eval-parsed)"),
+    make_option(c("-t", "--taxa"), type = "logical", default = FALSE, help = "Taxa flag (TRUE or FALSE)"),
+    make_option(c("-r", "--runs"), type = "integer", default = NULL, help = "Number of runs"),
+    make_option(c("-T", "--thresh"), type = "double", default = NULL, help = "Threshold value"),
+    make_option(c("-p", "--prop_thresh"), type = "double", default = NULL, help = "Proportional threshold value"),
+    make_option(c("-g", "--regression"), type = "double", default = NULL, help = "Regression value"),
+    make_option(c("-l", "--low_threshold"), type = "double", default = 40, help = "Low threshold [default: %default]"),
+    make_option(c("-u", "--up_threshold"), type = "double", default = 400, help = "Upper threshold [default: %default]")
+)
+
+# Parse arguments
+opt <- parse_args(OptionParser(option_list = option_list))
+
+# Read main input data
+microbe_data <- read.csv(opt$data_file, header = TRUE, stringsAsFactors = FALSE, check.names = FALSE)
+
+if (opt$mode == "decon") {
+    result <- decon(
+        data = microbe_data,
+        numb.blanks = opt$numb_blanks,
+        numb.ind = eval(parse(text = opt$numb_ind)),
+        taxa = opt$taxa,
+        runs = opt$runs,
+        thresh = opt$thresh,
+        prop.thresh = opt$prop_thresh,
+        regression = opt$regression,
+        low.threshold = opt$low_threshold,
+        up.threshold = opt$up_threshold
+    )
+    write.csv(result$decon.table, "decon_table.csv", row.names = FALSE)
+    write.csv(result$reads.removed, "reads_removed.csv", row.names = FALSE)
+    write.csv(result$sum.per.group, "difference_sum.csv", row.names = FALSE)
+    write.csv(result$mean.per.group, "difference_mean.csv", row.names = FALSE)
+    write.csv(result$OTUs.removed, "OTUs_removed.csv", row.names = FALSE)
+} else if (opt$mode == "remove_cont") {
+    result <- remove.cont(
+        data = microbe_data,
+        numb.blanks = opt$numb_blanks,
+        taxa = opt$taxa,
+        runs = opt$runs,
+        regression = opt$regression,
+        low.threshold = opt$low_threshold,
+        up.threshold = opt$up_threshold
+    )
+    write.csv(result, "decon_table.csv", row.names = FALSE)
+} else if (opt$mode == "remove_thresh") {
+    result <- remove.thresh(
+        data = microbe_data,
+        numb.ind = eval(parse(text = opt$numb_ind)),
+        taxa = opt$taxa,
+        thresh = opt$thresh,
+        prop.thresh = opt$prop_thresh
+    )
+    write.csv(result, "decon_table.csv", row.names = FALSE)
+} else if (opt$mode == "decon_diff") {
+    if (is.null(opt$output)) stop("Error: --output must be provided for decon.diff mode")
+    output_data <- read.csv(opt$output, header = TRUE, stringsAsFactors = FALSE, check.names = FALSE)
+    result <- decon.diff(
+        data = microbe_data,
+        output = output_data,
+        numb.blanks = opt$numb_blanks,
+        numb.ind = eval(parse(text = opt$numb_ind)),
+        taxa = opt$taxa
+    )
+    write.csv(result$decon.table, "decon_table.csv", row.names = FALSE)
+    write.csv(result$reads.removed, "reads_removed.csv", row.names = FALSE)
+    write.csv(result$sum.per.group, "difference_sum.csv", row.names = FALSE)
+    write.csv(result$mean.per.group, "difference_mean.csv", row.names = FALSE)
+    write.csv(result$OTUs.removed, "OTUs_removed.csv", row.names = FALSE)
+}