# HG changeset patch
# User galaxyp
# Date 1538037082 14400
# Node ID 22b661ec90410036791b0f783f45e88f512d68e0
# Parent  fec15a483a5c86eda143404713a4413eec708120
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 760ab8fdacac39fbebf1bfa3279e0156b48e164d

diff -r fec15a483a5c -r 22b661ec9041 searchgui.xml
--- a/searchgui.xml	Sat Sep 15 08:50:55 2018 -0400
+++ b/searchgui.xml	Thu Sep 27 04:31:22 2018 -0400
@@ -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>
@@ -25,16 +25,16 @@
 
         ## echo the search engines to run (single quotes important because X!Tandem)
         echo '$search_engines_options.engines';
-        echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}';
+        echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
 
         ##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;
 
         #for $mgf in $peak_lists:
-            #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
+            #set $input_name = $mgf.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
             ln -s -f '${mgf}' '${input_name}';
             #set $encoded_id = $__app__.security.encode_id($mgf.id)
-            echo 'Spectrums:${mgf.display_name}(API:${encoded_id})';
+            echo 'Spectrums:${mgf.element_identifier}(API:${encoded_id})';
         #end for
         ##ln -s "${input_database}" input_database.fasta;
         cp "${input_database}" input_database.fasta;