# HG changeset patch
# User iracooke
# Date 1444940399 14400
# Node ID 3ccfbb6730895f71dd2e82337ab1cc87788dd758
# Parent  d298e0b6fd72784ed722ac6fc84a1764ef94c29e
Update to PS 1.1 and SG 2.1.1

diff -r d298e0b6fd72 -r 3ccfbb673089 macros.xml
--- a/macros.xml	Tue Aug 11 15:55:30 2015 -0400
+++ b/macros.xml	Thu Oct 15 16:19:59 2015 -0400
@@ -25,7 +25,8 @@
             -fi $forward_ion
             -ri $reverse_ion
     </token>
-
+    <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
+    <token name="@SEARCH_GUI_VERION@">2.1</token>
     <xml name="general_options">
         <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
             help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
diff -r d298e0b6fd72 -r 3ccfbb673089 peptide_shaker.xml
--- a/peptide_shaker.xml	Tue Aug 11 15:55:30 2015 -0400
+++ b/peptide_shaker.xml	Thu Oct 15 16:19:59 2015 -0400
@@ -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>
@@ -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="">
diff -r d298e0b6fd72 -r 3ccfbb673089 searchgui.xml
--- a/searchgui.xml	Tue Aug 11 15:55:30 2015 -0400
+++ b/searchgui.xml	Thu Oct 15 16:19:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="1.28.0">
+<tool id="search_gui" name="Search GUI" version="2.1.1">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.28">searchgui</requirement>
+        <requirement type="package" version="2.1">searchgui</requirement>
         <environment_variable name="LC_ALL" action="set_to">C</environment_variable>        
     </requirements>
     <expand macro="stdio" />
@@ -22,6 +22,9 @@
         cwd=`pwd`;
         export HOME=\$cwd;
 
+        # Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
+        echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
+
         cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
         tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
 
@@ -330,6 +333,10 @@
 
         &&
 
+        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr)
+
+        &&
+
         exit_code_for_galaxy=\$?;
         cat $temp_stderr 2>&1;
         (exit \$exit_code_for_galaxy)