--- a/ms_data_converter.xml	Wed Mar 11 11:36:26 2015 -0400
+++ b/ms_data_converter.xml	Wed Mar 11 16:47:12 2015 -0500
@@ -18,16 +18,18 @@
     #end if
     --input="${input.extra_files_path}/wiff"
     --input_name="${basename}.wiff"
-    #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_scan')):
+    #### The os.path.exist did not work on Windows
+    ## #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_scan')):
       --implicit="${input.extra_files_path}/wiff_scan"
       --input="${input.extra_files_path}/wiff_scan"
       --input_name="${basename}.wiff.scan"
-    #end if
-    #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_mtd')):
+    ## #end if
+    #### The os.path.exist did not work on Windows
+    ## #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_mtd')):
       --implicit="${input.extra_files_path}/wiff_mtd"
       --input="${input.extra_files_path}/wiff_mtd"
       --input_name="${basename}.wiff.mtd"
-    #end if
+    ## #end if
     --output=${output}
     ## BEGIN_VERSION_DEFAULT
     --fromextension=$ext
@@ -39,6 +41,7 @@
     --binaryencoding=${result.precision}
     --index=${result.index}
     #end if
+    --debug
   </command>
 
   <inputs>