diff metaMS_cmd_interface.r @ 5:128509e27429

fixes

--- a/metaMS_cmd_interface.r	Fri Oct 24 16:51:42 2014 +0200
+++ b/metaMS_cmd_interface.r	Fri Oct 24 17:03:39 2014 +0200
@@ -4,18 +4,18 @@
 args.constructedDB <- args[1]
 ## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
 args.dataZip <- args[2]
-args.zipExtrDir <- args[3]
+args.zipExtrDir <- paste(args[2],"dir/")
 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings" 
-args.settings <- args[4]
+args.settings <- args[3]
 
 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
-args.outAnnotationTable <- args[5]
-args.outLogFile <- args[6]
-args.xsetOut <- args[7]
+args.outAnnotationTable <- args[4]
+args.outLogFile <- args[5]
+args.xsetOut <- args[6]
 
 ## report files
-args.htmlReportFile <- args[8]
-args.htmlReportFile.files_path <- args[9]
+args.htmlReportFile <- args[7]
+args.htmlReportFile.files_path <- args[8]
 
 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
 msg <- file(args.outLogFile, open="wt")