diff sequenza_pipeline.R @ 0:73338a1805e7 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequenza_pipeline.R	Tue Oct 11 14:31:59 2016 -0400
@@ -0,0 +1,37 @@
+#!/usr/bin/R
+
+# Script to Run Sequenza Pipeline in Galaxy
+library(sequenza);
+
+# INPUT FILE
+args=(commandArgs(TRUE));
+input.file <- args[1];
+
+ploidy <- args[4];
+
+cellularity <-args[5];
+
+# STEP ONE
+extract.data <- sequenza.extract(
+file=input.file,
+gz=TRUE
+);
+
+# STEP TWO
+fit.data <- sequenza.fit(
+extract.data
+);
+
+# STEP THREE
+if(length(args)>3){
+
+results.data <- sequenza.results(extract.data, cellularity=cellularity, ploidy=ploidy,out.dir = args[3],sample.id = args[2]);
+
+} else{
+  results.data <- sequenza.results(
+extract.data,
+  fit.data,
+out.dir = args[3],
+  sample.id = args[2]
+);
+}