--- a/pepquery2.xml	Wed Oct 18 06:40:40 2023 +0000
+++ b/pepquery2.xml	Wed May 08 17:12:21 2024 +0000
@@ -159,7 +159,7 @@
             </param>
             <when value="novel"/> 
             <when value="known"> 
-                 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
+                 <param argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
             </when>
         </conditional>
         <section name="req_inputs" title="Input Data" expanded="true">
@@ -257,7 +257,7 @@
                     <option value="public">public proteomics data repositories</option>
                 </param>
                 <when value="history">
-                    <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
+                    <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML" />
                 </when>
                 <when value="indexed">
                     <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
@@ -276,7 +276,7 @@
                 </when>
             </conditional>
 
-            <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
+            <param argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
                 <option value="1">index (1-based) in MGF</option>
                 <option value="2">spectrum title in MGF</option>
             </param>
@@ -307,7 +307,7 @@
 
              <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications  Default: 3" />
              <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
-             <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
+             <param argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
         </section>
 
         <section name="digestion" title="Digestion" expanded="false">
@@ -369,7 +369,7 @@
             <option value="ptm_detail.txt">ptm_detail.txt</option>
             <option value="ms_index">MS/MS Index</option>
         </param>
-        <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
+        <param argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
     </inputs>
     <outputs>
         <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">