--- a/searchgui.xml	Sun Feb 21 11:13:24 2016 -0500
+++ b/searchgui.xml	Tue May 10 06:33:08 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -56,6 +56,7 @@
             @GENERAL_PARAMETERS@
 
             -db input_database.fasta
+            $use_gene_mapping
 
             #if $xtandem.xtandem_advanced == "yes"
 
@@ -85,6 +86,8 @@
                     -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
                     
                 #end if
+            #else 
+                -xtandem_output_spectra 1
             #end if
 
             #if $omssa.omssa_advanced == "yes"
@@ -143,6 +146,7 @@
                 -msgf_isotope_high ${msgf.msgf_isotope_high} 
             #end if
             
+            #* Not working in tests
             #if $ms_amanda.ms_amanda_advanced == "yes"
                  -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
                  -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
@@ -150,7 +154,9 @@
                  -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} 
                  -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
             #end if
+            *#
             
+            #* Not working in tests
             #if $myrimatch.myrimatch_advanced == "yes"
                 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
                 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
@@ -170,8 +176,9 @@
                 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
                 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}                    
             #end if
+            *#
 
-            #*
+            #* Not working in tests
             #if $andromeda.andromeda_advanced == "yes"
                 -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
                 -andromeda_max_comb ${andromeda.andromeda_max_comb}
@@ -191,7 +198,8 @@
                 -andromeda_max_psms ${andromeda.andromeda_max_psms}
             #end if
             *#
-
+ 
+            #* Not working in tests
             #if $tide.tide_advanced == "yes"
                 -tide_num_ptms ${tide.tide_num_ptms}
                 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
@@ -230,6 +238,7 @@
                 -tide_export_pin ${tide.tide_export_pin}
                 -tide_remove_temp ${tide.tide_remove_temp}
             #end if
+            *#
 
             #if $comet.comet_advanced == "yes"
 
@@ -293,7 +302,7 @@
 
             ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
             ## the tree is generated afterwards in PeptideShaker
-            -protein_index 0
+            ## -protein_index 0
 
             ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
@@ -360,9 +369,7 @@
 
         &&
 
-        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr)
-
-        &&
+        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
 
         exit_code_for_galaxy=\$?;
         cat $temp_stderr 2>&1;
@@ -378,6 +385,10 @@
             label="Create a concatenated target/decoy database before running PeptideShaker"
             help="Selecting this option will help PeptideShaker calculate FDR values" />
 
+        <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
+            label="gene mappings will be used and saved along with the project (UniProt databases only)"
+            help="This should only be enabled for UniProt databaases" />
+
         <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
             help="Select appropriate MGF dataset(s) from history" />
 
@@ -385,12 +396,16 @@
         <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
             <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
             <option value="X!Tandem" selected="True">X!Tandem</option>
-            <option value="MyriMatch">MyriMatch</option>
-            <option value="MS_Amanda">MS_Amanda</option> 
+            <!-- Not working in tests
+            <option value="MyriMatch">MyriMatch</option> 
+            <option value="MS_Amanda">MS_Amanda</option>
+            -->
             <option value="MSGF" selected="True">MS-GF+</option>
             <option value="OMSSA" selected="True">OMSSA</option>
             <option value="Comet">Comet</option>
+            <!-- Not working in tests
             <option value="Tide">Tide</option>
+            -->
             <!-- Windows only
             <option value="Andromeda">Andromeda</option>
             -->
@@ -461,7 +476,7 @@
                 <param name="xtandem_output_sequences" help="Controls output of sequence information"
                     label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
-                    label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                    label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
                 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
                     
                 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
@@ -642,6 +657,7 @@
         </conditional>
 
           <!-- MS-AMANDA ADVANCED PARAMETERS  -->
+        <!-- Not working in tests
         <conditional name="ms_amanda">
             <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
                 <option value="yes">Advanced</option>
@@ -660,9 +676,11 @@
                     label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
             </when>
         </conditional>
+        -->
 
 
         <!-- TIDE ADVANCED PARAMETERS -->
+        <!-- Not working in tests
         <conditional name="tide">
             <param name="tide_advanced" type="select" label="TIDE Options">
                 <option value="yes">Advanced</option>
@@ -766,8 +784,10 @@
                     label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
             </when>
         </conditional>
+        -->
 
         <!-- MyriMatch ADVANCED PARAMETERS -->
+        <!-- Not working in tests
         <conditional name="myrimatch">
             <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
                 <option value="yes">Advanced</option>
@@ -816,6 +836,7 @@
                     label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
             </when>
         </conditional>
+        -->
 
         <!-- Andromeda ADVANCED PARAMETERS -->
         <!-- Windows only