# HG changeset patch
# User morinlab
# Date 1476209905 14400
# Node ID 75c4a4c32baee7501d9dbdb2726d4c8f50b806f0
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
diff -r 000000000000 -r 75c4a4c32bae correctReads.R
--- /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")
diff -r 000000000000 -r 75c4a4c32bae correctReads.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/correctReads.xml Tue Oct 11 14:18:25 2016 -0400
@@ -0,0 +1,32 @@
+
+
+ Correct Read Counter for GC content and mappability biases
+
+
+ Rscript
+ TitanCNA
+ R
+ titancna
+
+
+
+ Rscript $__tool_directory__/correctReads.R $tumour $normal $gc $map
+ #if $target:
+ $target
+ #else:
+ NULL
+ #end if
+ $output 2>&1
+
+
+
+
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+
diff -r 000000000000 -r 75c4a4c32bae tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Oct 11 14:18:25 2016 -0400
@@ -0,0 +1,6 @@
+
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+