--- a/msgfplus_search.xml	Wed Jun 25 19:00:11 2014 -0400
+++ b/msgfplus_search.xml	Wed Jun 25 23:03:32 2014 -0400
@@ -34,7 +34,6 @@
         --precursor-ion-tol-units=$precursor_tolu 
         -v $missed_cleavages
         $cleavage_semi
-        -f $fragment_ion_tol 
         -p $precursor_ion_tol 
         --instrument=$instrument
         --isotope-error-range=$isotope_error_range
@@ -48,7 +47,7 @@
         --java-mem=$java_mem
         #if $pepxml_output_use:
         --pepxml
-        #end unless
+        #end if
     </command>
 
     <inputs>
@@ -70,7 +69,7 @@
                 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
             </when>
         </conditional>
-        <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
+        <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
         <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
             <options from_file="msgfplus_mods.loc">
                 <column name="name" index="0" />
@@ -138,8 +137,6 @@
             <option value="3">iTRAQPhospho</option>
         </param>
 
-        <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
-
         <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
         <param name="precursor_tolu" type="select" format="text">
             <label>Precursor Ion Tolerance Units</label>