--- a/msconvert_macros.xml	Sat Feb 23 06:25:48 2019 -0500
+++ b/msconvert_macros.xml	Thu Feb 28 14:14:44 2019 -0500
@@ -9,19 +9,30 @@
     #set $ext = $input.ext
 
     ## sanitize display name for use as temp filename
-    #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier)
+    #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
 
     #if $ext == 'wiff':
       ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
       ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
+      #set inputmask = "'"+$basename+"'"
     #elif $ext.endswith('tar'):
       ln -s '$input' '${basename}' &&
       tar xf '${basename}' &&
       #set basename = $os.path.splitext($basename)[0]
+      #if $ext.startswith('waters'):
+        #set inputmask = '*.raw'
+      #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
+        #set inputmask = '*.d'
+      #elif $ext.startswith('wiff'):
+        #set inputmask = '*.wiff *.wiff2'
+      #else
+        #raise RuntimeError("Unrecognized type of tar (${ext})")
+      #end if
     #else
       ln -s '$input' '${basename}' &&
+      #set inputmask = "'"+$basename+"'"
     #end if
-    
+
     #if $data_processing.precursor_refinement.use_mzrefinement
       #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
       #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
@@ -31,7 +42,7 @@
     uid=`id -u` &&
     gid=`id -g` &&
 
-    wine64_anyuser msconvert '${basename}'
+    wine64_anyuser msconvert ${inputmask}
     --outdir outputs
     --${output_type}