--- a/proteinpilot.xml	Wed Dec 19 00:22:55 2012 -0500
+++ b/proteinpilot.xml	Fri May 10 18:04:15 2013 -0400
@@ -1,13 +1,19 @@
 <tool id="proteinpilot" version="0.2.1" name="ProteinPilot">
   <description></description>
   <!-- ESCAPE input and database name -->
+  <configfiles>
+    <configfile name="input_config">## Describe input groups
+group:DEFAULT_GROUP
+#for $input in $inputs:
+name:${input.display_name}
+path:${input}
+#end for
+</configfile>
+  </configfiles>  
   <command interpreter="python">proteinpilot_wrapper.py 
-    #for $input in $inputs:
-    --input="${input}"
-    --input_name="${input.name}"
-    #end for
+    --input_config="$input_config"
     --database="${database}"
-    --database_name="${database.name}"
+    --database_name="${database.display_name}"
     --output=$output
     --output_methods=$output_methods
     --sample_type="$sample_type"
@@ -38,6 +44,10 @@
       <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option>
       <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option>
       <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option>
+      <option value="TMT6plex ID-only (Peptide Labeled)">TMT6plex ID-only (Peptide Labeled)</option>
+      <option value="TMT6plex ID-only (Protein Labeled)">TMT6plex ID-only (Protein Labeled)</option>
+      <option value="TMT2plex ID-only (Peptide Labeled)">TMT2plex ID-only (Peptide Labeled)</option>
+      <option value="TMT ID-only (Peptide Labeled)">TMT ID-only (Peptide Labeled)</option>
       <option value="mTRAQ (Peptide Labeled - M00, M04)">mTRAQ (Peptide Labeled - M00, M04)</option>
       <option value="mTRAQ (Peptide Labeled - M00, M08)">mTRAQ (Peptide Labeled - M00, M08)</option>
       <option value="mTRAQ (Peptide Labeled - M04, M08)">mTRAQ (Peptide Labeled - M04, M08)</option>
@@ -62,7 +72,7 @@
       <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
       <UI_QUANT_TYPE></UI_QUANT_TYPE>
       
-      <UI_SAMPLE_TYPE>TMT6plex ID-only (Protein Labeled)</UI_SAMPLE_TYPE>
+      <UI_SAMPLE_TYPE></UI_SAMPLE_TYPE>
       <UI_QUANT_TYPE></UI_QUANT_TYPE>
 
       <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
@@ -107,6 +117,7 @@
       <option value="Lys C + Glu C">Lys C + Glu C</option>
       <option value="Glu C + Asp N">Glu C + Asp N</option>
       <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option>
+      <option value="None">None</option>
     </param>
     <param type="select" name="instrument" label="Instrument">
       <option value="TripleTOF 5600">TripleTOF 5600</option>