# HG changeset patch
# User galaxyp
# Date 1488219367 18000
# Node ID 5b89d74c9f2ae69319ef7e180db76263769c3c44
# Parent  bc85e2c497391aa042633499713017ef02c2a813
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit a9c70724c3561247e91f0b69b35022adcf3445ff

diff -r bc85e2c49739 -r 5b89d74c9f2a searchgui.xml
--- a/searchgui.xml	Thu Feb 16 07:37:13 2017 -0500
+++ b/searchgui.xml	Mon Feb 27 13:16:07 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>
@@ -59,9 +59,11 @@
             @GENERAL_PARAMETERS@
 
             -db input_database.fasta
+            $protein_database_options.use_gene_mapping
             #if $protein_database_options.use_gene_mapping:
-                $protein_database_options.use_gene_mapping
                 $protein_database_options.update_gene_mapping
+            #else:
+                -updateGeneMapping 0
             #end if
 
             #if $advanced_options.xtandem.xtandem_advanced == "yes"