diff correctReads.R @ 0:75c4a4c32bae draft default tip

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correctReads.R	Tue Oct 11 14:18:25 2016 -0400
@@ -0,0 +1,21 @@
+library(TitanCNA)
+version <- "0.1.1"
+args <- commandArgs(TRUE)
+
+tumWig <- args[1]
+normWig <- args[2]
+gc <- args[3]
+map <- args[4]
+target_list <- args[5]
+outfile <- args[6]
+
+message('titan: Correcting GC content and mappability biases...')
+
+if( !is.null(target_list) ){
+    target_list_data <- read.table(target_list, sep="\t", header=F, stringsAsFactors=F) 
+    cnData <- correctReadDepth(tumWig, normWig, gc, map, targetedSequence = target_list_data)
+} else {
+    cnData <- correctReadDepth(tumWig, normWig, gc, map)
+}
+
+write.table(cnData, file = outfile, col.names = TRUE, row.names = FALSE, quote = FALSE, sep ="\t")