--- a/protein_quantifier.xml	Fri May 10 17:31:59 2013 -0400
+++ b/protein_quantifier.xml	Wed Jun 19 13:15:44 2013 -0400
@@ -23,7 +23,18 @@
 </configfile>
   </configfiles>
   <inputs>
-    <expand macro="map_input" />
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="featurexml">Features (FeatureXML)</option>
+        <option value="consensusxml">Consensus (ConsensusXML)</option>
+      </param>
+      <when value="featurexml">
+        <param format="featurexml" name="map_input" type="data" label="Input Features" />
+      </when>
+      <when value="consensusxml">
+        <param format="consensusxml" name="map_input" type="data" label="Input Consensus" />
+      </when>
+    </conditional>
     <conditional name="protein_prophet">
       <param name="use" label="Use ProteinProphet Results (converted to idXML)" help="For information about indistinguishable proteins." type="boolean" />
       <when value="false">
@@ -32,7 +43,7 @@
         <param name="protxml" label="Protein/Peptide Identifications Input" type="data" format="idxml" />
       </when>
     </conditional>
-    <param name="top" label="Top" value="0" type="integer" />
+    <param name="top" label="Top" value="3" type="integer" help="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all) (default: '3' min: '0')" />
   </inputs>
   <outputs>
     <data format="tabular" name="protein_output" />