--- a/msconvert.xml	Fri Sep 26 14:44:54 2014 -0400
+++ b/msconvert.xml	Wed Dec 07 16:43:07 2016 -0500
@@ -8,11 +8,24 @@
   </requirements>
 -->
   <command interpreter="python">
+    #import re
     #set $ext = $input.ext
     msconvert_wrapper.py
-    --input=${input}
-    #if hasattr($input, 'display_name')
-    --input_name='${input.display_name}'
+    #if $type.input_type == 'wiff':
+      #set basename = 'absciex'
+      #if hasattr($input, 'display_name')
+        #set basename = $re.sub('\W','_',$input.display_name)
+      #end if
+      --input=${input.extra_files_path}/wiff
+      --input_name='${basename}.wiff
+      --implicit=${input.extra_files_path}/wiff_scan
+      --input=${input.extra_files_path}/wiff_scan
+      --input_name='${basename}.wiff.scan
+    #else
+      --input=${input}
+      #if hasattr($input, 'display_name')
+      --input_name='${input.display_name}'
+      #end if
     #end if
     --output=${output}
     ## BEGIN_VERSION_DEFAULT
@@ -122,6 +135,7 @@
         <option value="mzxml">mzXML</option>
         <option value="mgf">mgf</option>
         <option value="ms2">ms2</option>
+        <option value="wiff">wiff</option>
       </param>
       <when value="mzml">
         <param format="mzml" name="input" type="data" label="Input mzML"/>
@@ -135,6 +149,9 @@
       <when value="ms2">
         <param format="ms2" name="input" type="data" label="Input ms2"/>
       </when>
+      <when value="wiff">
+        <param format="wiff" name="input" type="data" label="Input wiff"/>
+      </when>
     </conditional>
     <!-- END_VERSION_DEFAULT -->
     <param name="output_type" type="select" label="Output Type">
@@ -347,7 +364,7 @@
 
   </inputs>
   <outputs>
-    <data format="mzml" name="output">
+    <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" >
       <change_format>
         <when input="output_type" value="mzXML" format="mzxml" />
         <when input="output_type" value="unindexed_mzXML" format="mzxml" />