--- a/strelka_wrapper.py	Wed Oct 01 13:45:33 2014 +0200
+++ b/strelka_wrapper.py	Wed Oct 15 14:43:12 2014 +0200
@@ -61,30 +61,30 @@
     print(os.environ['PATH'])
     parser = argparse.ArgumentParser()                                             
     parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
-    parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )   
-    parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False )
-    parser.add_argument( '-c', '--configFile', help='path to tumor bam file', required = False )
-    parser.add_argument( '--depthFilterMultiple', help='path to tumor bam file', required = False )
-    parser.add_argument( '--snvMaxFilteredBasecallFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--snvMaxSpanningDeletionFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--indelMaxRefRepeat', help='path to tumor bam file', required = False )
-    parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--indelMaxIntHpolLength', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvPrior', help='path to tumor bam file', required = False )
-    parser.add_argument( '--sindelPrior', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvNoise', help='path to tumor bam file', required = False )
-    parser.add_argument( '--sindelNoise', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--minTier1Mapq', help='path to tumor bam file', required = False )
-    parser.add_argument( '--minTier2Mapq', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvQuality_LowerBound', help='path to tumor bam file', required = False )
-    parser.add_argument( '--sindelQuality_LowerBound', help='path to tumor bam file', required = False )
-    parser.add_argument( '--isWriteRealignedBam', help='path to tumor bam file', required = False )
+    parser.add_argument( '-n', '--normalBam', help='', required = False )   
+    parser.add_argument( '-r', '--refFile', help='', required = False )
+    parser.add_argument( '-c', '--configFile', help='', required = False )
+    parser.add_argument( '--depthFilterMultiple', help='', required = False )
+    parser.add_argument( '--snvMaxFilteredBasecallFrac', help='', required = False )
+    parser.add_argument( '--snvMaxSpanningDeletionFrac', help='', required = False )
+    parser.add_argument( '--indelMaxRefRepeat', help='', required = False )
+    parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='', required = False )
+    parser.add_argument( '--indelMaxIntHpolLength', help='', required = False )
+    parser.add_argument( '--ssnvPrior', help='', required = False )
+    parser.add_argument( '--sindelPrior', help='', required = False )
+    parser.add_argument( '--ssnvNoise', help='', required = False )
+    parser.add_argument( '--sindelNoise', help='', required = False )
+    parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='', required = False )
+    parser.add_argument( '--minTier1Mapq', help='', required = False )
+    parser.add_argument( '--minTier2Mapq', help='', required = False )
+    parser.add_argument( '--ssnvQuality_LowerBound', help='', required = False )
+    parser.add_argument( '--sindelQuality_LowerBound', help='', required = False )
+    parser.add_argument( '--isWriteRealignedBam', help='', required = False )
     parser.add_argument( '--binSize', help='path to tumor bam file', required = False )
-    parser.add_argument( '--extraStrelkaArguments', help='path to tumor bam file', required = False )
-    parser.add_argument( '--isSkipDepthFilters', help='path to tumor bam file', required = False )
-    parser.add_argument( '--maxInputDepth', help='path to tumor bam file', required = False )
-    parser.add_argument( '--scriptPath', help='path to tumor bam file', required = False )
+    parser.add_argument( '--extraStrelkaArguments', help='', required = False )
+    parser.add_argument( '--isSkipDepthFilters', help='', required = False )
+    parser.add_argument( '--maxInputDepth', help='', required = False )
+    parser.add_argument( '--scriptPath', help='', required = False )
     args = parser.parse_args()
 
     root_dir= args.scriptPath
@@ -115,8 +115,8 @@
     #creating config file if needed
     if args.configFile == "Custom":
     	_create_config(vars(args), config_ini)
-    elif args.configFile == "Default":
-        cmdbash="cp %s %s" % (root_dir + "/strelka_config.sample", config_ini)
+    elif args.configFile in ["strelka_config_bwa_default.ini", "strelka_config_isaac_default.ini", "strelka_config_eland_default.ini"]:
+        cmdbash="cp %s %s" % (root_dir + "/lib/" + args.configFile, config_ini)
         my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
     else:
     	if not os.path.exists(args.configFile):