--- a/morpheus.xml	Thu Nov 05 09:22:08 2015 -0500
+++ b/morpheus.xml	Thu Nov 19 16:02:50 2015 -0500
@@ -1,9 +1,7 @@
-<tool id="morpheus" name="Morpheus" version="1.171.1">
+<tool id="morpheus" name="Morpheus" version="1.171.2">
     <description>database search algorithm for high-resolution tandem mass spectra</description>
     <macros>
         <xml name="modification_options">
-            <option value="carbamidomethylation of C">carbamidomethylation of C</option>
-            <option value="oxidation of M">oxidation of M</option>
             <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option>
             <option value="acetylation of lysine">acetylation of lysine</option>
             <option value="phosphorylation of S">phosphorylation of S</option>
@@ -30,6 +28,16 @@
             <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option>
             <option value="iTRAQ 8-plex on Y    ">iTRAQ 8-plex on Y    </option>
         </xml>
+        <xml name="variable_modification_options">
+            <option value="oxidation of M" selected="true">oxidation of M</option>
+            <option value="carbamidomethylation of C">carbamidomethylation of C</option>
+            <expand macro="modification_options"/>
+        </xml>
+        <xml name="fixed_modification_options">
+            <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option>
+            <option value="oxidation of M">oxidation of M</option>
+            <expand macro="modification_options"/>
+        </xml>
     </macros>
 
     <requirements>
@@ -70,9 +78,6 @@
         #if  str($mvmi) != '':
             -mvmi=$mvmi
         #end if
-        #if  str($precmt) != 'None':
-            -precmt=$precmt
-        #end if
         #if  str($precmtv) != '':
             -precmtv=$precmtv
         #end if
@@ -80,6 +85,9 @@
             -precmtu=$precmtu
         #end if
         #if str( $advanced.adv_options_selector) == "set":
+            #if  str($advanced.precmt) != 'None':
+                -precmt=$advanced.precmt
+            #end if
             #if  str($advanced.minprecz) != '':
                 -minprecz=$advanced.minprecz
             #end if
@@ -139,17 +147,13 @@
         <param name="input" type="data" format="mzml" label='Indexed mzML' />
         <param name="searchdb" type="data" format="fasta,uniprotxml" label="MS Protein Search Database: UniProt Xml or Fasta"/>
         <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications">
-            <expand macro="modification_options" />
+            <expand macro="fixed_modification_options" />
         </param>
         <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications">
-            <expand macro="modification_options" />
+            <expand macro="variable_modification_options" />
         </param>
         <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" />
         <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" />
-        <param name="precmt" type="select" optional="true" label="Precursor Mass Type">
-            <option value="Monoisotopic">Monoisotopic</option>
-            <option value="Average">Average</option>
-        </param>
         <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" />
         <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units">
             <option value="ppm" selected="true">ppm</option>
@@ -161,18 +165,22 @@
                 <option value="do_not_set" selected="True">Do not set</option>
             </param>
             <when value="set">
+                <param name="precmt" type="select" optional="true" label="Precursor Mass Type">
+                    <option value="Monoisotopic">Monoisotopic</option>
+                    <option value="Average">Average</option>
+                </param>
                 <param name="noup" type="boolean" truevalue="" falsevalue="-noup=True" checked="True" label="Use G-PTM with Uniprot Proteome Search Databases" />
                 <param name="minprecz" type="integer" value="2" optional="true" label="Minimum Unknown Precursor Charge State" />
                 <param name="maxprecz" type="integer" value="4" optional="true" label="Maximum Unknown Precursor Charge State" />
                 <param name="at" type="float" value="" optional="true" min="0.0" label="Absolute MS/MS Intensity Threshold" />
                 <param name="rt" type="float" value="" optional="true" min="0.0" label="Relative MS/MS Intensity Threshold" />
-                <param name="mp" type="integer" value="" optional="true" min="-1" label="Maximum Number of MS/MS Peaks" help="to disable set to: -1"/>
+                <param name="mp" type="integer" value="400" optional="true" min="-1" label="Maximum Number of MS/MS Peaks" help="to disable set to: -1"/>
                 <param name="acs" type="boolean" truevalue="-acs=True" falsevalue="-acs=False" checked="true" optional="true" label="Assign Charge States" />
-                <param name="di" type="boolean" truevalue="-di=True" falsevalue="-di=False" checked="true" optional="true" label="Deisotope" />
-                <param name="ad" type="select" optional="true" label="Append Decoys on the fly" 
+                <param name="di" type="boolean" truevalue="-di=True" falsevalue="-di=False" checked="false" optional="true" label="Deisotope" />
+                <param name="ad" type="select" optional="true" label="Create Target-Decoy Database On The Fly" 
                        help="Set to No if Search Database ia a fasta that already includes decoys.">
+                    <option value="True" selected="true">Yes</option>
                     <option value="False">No</option>
-                    <option value="True">Yes</option>
                 </param>
                 <param name="mmc" type="integer" value="2" optional="true" min="0" max="20" label="Maximum Missed Cleavages" />
                 <param name="pmc" type="boolean" truevalue="-pmc=True" falsevalue="-pmc=False" checked="false" optional="true" label="Precursor Monoisotopic Peak Correction" />
@@ -192,7 +200,7 @@
                     <option value="Retain">Retain</option>
                     <option value="Cleave">Cleave</option>
                 </param>
-                <param name="cmu" type="boolean" truevalue="-cmu=True" falsevalue="-cmu=False" checked="false" optional="true" label="Consider Modifications Unique" />
+                <param name="cmu" type="boolean" truevalue="-cmu=True" falsevalue="-cmu=False" checked="false" optional="true" label="Consider Modified Forms as Unique Peptides" />
                 <param name="mmu" type="boolean" truevalue="-mmu=True" falsevalue="-mmu=False" checked="false" optional="true" label="Minimize Memory Usage" />
             </when>
             <when value="do_not_set"/>