--- a/searchgui.xml	Wed Jan 20 13:29:07 2021 +0000
+++ b/searchgui.xml	Tue Mar 16 15:12:03 2021 +0000
@@ -1,4 +1,8 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@">
+<tool id="search_gui"
+      name="Search GUI"
+      version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@"
+      profile="20.01"
+>
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -11,24 +15,24 @@
     </requirements>
     <expand macro="stdio" />
     <command use_shared_home="false">
+
 <![CDATA[
         #from datetime import datetime
         #import json
         #import os
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
-        #set $temp_stderr = "searchgui_stderr"
         #set $bin_dir = "bin"
 
         mkdir output;
         mkdir output_reports;
         mkdir temp_folder;
         mkdir log_folder;
+        trap ">&2 cat log_folder/*.log" EXIT;
+
         cwd=`pwd`;
         export HOME=\$cwd;
 
-        echo "" > $temp_stderr &&
-
         ## echo the search engines to run (single quotes important because X!Tandem)
         echo '$search_engines_options.engines';
         echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}';
@@ -59,7 +63,7 @@
         ## Search CLI ##
         ################
         echo 'running search gui' &&
-        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
             -spectrum_files \$cwd
             -fasta_file "\$cwd/input_fasta_file.fasta"
@@ -150,17 +154,17 @@
             ## mgf and database in output
             -output_data 1
 
-        2>> $temp_stderr)
+        &&
+
+        echo '>log_folder:' &&
+
+        ls -l \$cwd/log_folder &&
+
+        mv output/searchgui_out.zip searchgui_out.zip
 
         &&
 
-        (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
-
-        &&
-
-        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
-
-        cat $temp_stderr 2>&1;
+        zip -u searchgui_out.zip searchgui.properties
 ]]>
     </command>
     <inputs>