# HG changeset patch
# User crs4
# Date 1528723964 14400
# Node ID 9ccde1867fbbd3ae060d37e3144d8d06b4974617
# Parent  88b89f435f6a74fc6c3dd6a4a76483aeab9eb40e
Replaces Rscript by R CMD BATCH

diff -r 88b89f435f6a -r 9ccde1867fbb exomedepth.R
--- a/exomedepth.R	Tue Jun 05 18:58:08 2018 -0400
+++ b/exomedepth.R	Mon Jun 11 09:32:44 2018 -0400
@@ -3,7 +3,8 @@
 
 # Import parameters from xml wrapper (args_file)
 args  <- commandArgs(trailingOnly=TRUE)
-param <- read.table(args[1],sep="=", as.is=TRUE)
+eval(parse(text=args[[1]]))
+param <- read.table(mypars,sep="=", as.is=TRUE)
 
 # Set common parameters
 target      <- param[match("target",param[,1]),2]