--- a/peptide_shaker.xml	Mon Aug 10 18:25:37 2015 -0400
+++ b/peptide_shaker.xml	Fri Nov 06 15:33:34 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.40">peptide_shaker</requirement>
+        <requirement type="package" version="1.1">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -33,7 +33,7 @@
             -sample '$samp_str'
             -replicate 1
             -identification_files \$cwd/searchgui_input.zip
-            -out \$cwd/peptideshaker_output.cps
+            -out \$cwd/peptideshaker_output.cpsx
             -zip \$cwd/peptideshaker_output.zip
 
             -threads "\${GALAXY_SLOTS:-12}"
@@ -166,7 +166,12 @@
     </command>
     <inputs>
         <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
-            help="SearchGUI Results from History"/>
+            help="SearchGUI Results from History">
+            <options options_filter_attribute="metadata.searchgui_major_version" >
+                <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
+            </options>
+            <validator type="expression" message="This version of PeptideShaker will only work with SearchGUI version: @SEARCHGUI_MAJOR_VERSION@ .">value is not None and value.metadata.searchgui_major_version == "@SEARCHGUI_MAJOR_VERSION@"</validator>
+        </param>
 
         <conditional name="species_type">
             <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
@@ -178,6 +183,7 @@
                 <option value="Protists">Protists</option>
                 <option value="no_species_type" selected="true">No species restriction</option>
             </param>
+            <when value="no_species_type"/>
             <when value="Protists">
                 <param name="species" type="select" label="The species to use for the gene annotation"
                     help="">