--- a/searchgui.xml	Wed Jan 18 16:43:44 2017 -0500
+++ b/searchgui.xml	Wed Jan 25 15:37:43 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -101,9 +101,7 @@
                 -omssa_remove_prec ${omssa.remove_precursor}
                 -omssa_scale_prec ${omssa.scale_precursor}
                 -omssa_estimate_charge ${omssa.estimate_charge}
-
                 -omssa_memory ${omssa.omssa_memory}
-                ## -omssa_isotopes ${omssa.omssa_isotopes} 
                 -omssa_neutron ${omssa.omssa_neutron} 
                 -omssa_low_intensity "${omssa.omssa_low_intensity}" 
                 -omssa_high_intensity ${omssa.omssa_high_intensity} 
@@ -148,8 +146,6 @@
                 -msgf_protocol ${msgf.msgf_protocol} 
                 -msgf_num_matches ${msgf.msgf_num_matches} 
                 -msgf_additional ${msgf.msgf_additional} 
-                -msgf_isotope_low ${msgf.msgf_isotope_low} 
-                -msgf_isotope_high ${msgf.msgf_isotope_high} 
             #end if
             
             #* Not working in tests
@@ -168,8 +164,6 @@
                 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
                 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
                 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
-                -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
-                -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
                 -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
                 -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
                 -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
@@ -581,9 +575,7 @@
                 
                 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
                     label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
-                  <!-- param name="omssa_isotopes" type="integer" value="0" 
-                      label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
-                   <param name="omssa_neutron" type="float" value="1446.94" 
+                <param name="omssa_neutron" type="float" value="1446.94" 
                        label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
                 <param name="omssa_low_intensity" type="float" value="0.0" 
                     label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
@@ -712,8 +704,6 @@
                     <option value="0" selected="True">output basic scores only</option>
                     <option value="1" >output additional features</option>
                 </param>
-                <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
-                <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> 
             </when>
         </conditional>
 
@@ -864,10 +854,6 @@
                     label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
                 <param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
                     label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
-                <param name="myrimatch_isotope_low"  type="integer" value="-1"
-                    label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
-                <param name="myrimatch_isotope_high"  type="integer" value="2"
-                    label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
                 <param name="myrimatch_num_matches"  type="integer" value="10"
                     label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
                 <param name="myrimatch_num_ptms"  type="integer" value="2"
@@ -1099,7 +1085,6 @@
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
             <param name="xtandem.xtandem_advanced" value="yes"/>
             <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
-
             <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 
         </test>
         <!-- Test that search works with MSAmanda -->
@@ -1112,7 +1097,6 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="MS_Amanda"/>
-
             <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 
         </test>
     </tests>