--- a/peptide_shaker.xml	Wed Jan 20 13:29:07 2021 +0000
+++ b/peptide_shaker.xml	Tue Mar 16 15:12:03 2021 +0000
@@ -1,4 +1,9 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@">
+<tool id="peptide_shaker"
+      name="Peptide Shaker"
+      version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"
+      profile="20.01"
+>
+
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -11,22 +16,23 @@
         <requirement type="package">unzip</requirement>
     </requirements>
     <expand macro="stdio" />
-
-    <command><![CDATA[
-    ## When supporting more advanced Galaxy versions:    command use_shared_home="false"
+    <!-- TODO: check trap comment.
+    <command use_shared_home="false">
+-->
+    <command>
+<![CDATA[
         #from datetime import datetime
         #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 = "peptideshaker_stderr"
         #set $bin_dir = "bin"
         #set $exporting_followup_boolean = False
+        ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
+        ## trap ">&2 cat resources/*.log" EXIT;
 
         mkdir output_reports &&
         cwd=`pwd` &&
         export HOME=\$cwd &&
 
-        echo "" > $temp_stderr &&
-
         ln -s '$searchgui_input' searchgui_input.zip &&
 
         ## OPTIONAL MAIN PARAMETERS
@@ -64,7 +70,7 @@
         ######################
         ## PeptideShakerCLI ##
         ######################
-        (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
+        peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
             -gui 0
             -temp_folder \$cwd/PeptideShakerCLI
             -log \$cwd/resources
@@ -182,8 +188,6 @@
             #end if
         #end if
 
-        2>> $temp_stderr)
-
         ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
         #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
             ## This unzipping command creates a reports folder into the current folder!
@@ -238,6 +242,10 @@
             #if '11' in $output_reports_list:
                 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
             #end if
+            ## the last ; is removed from the generated command line
+            ## thus we need to make sure that the above `find ... -exec ... \;`
+            ## is not the last command
+            && true
         #end if
 
         ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip)
@@ -259,7 +267,6 @@
                 && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
             #end if
         #end if
-        && cat $temp_stderr 2>&1;
 ]]>
     </command>
     <inputs>
@@ -626,7 +633,6 @@
                       <has_line_matching expression="520.9862671 4666.4399414063"/>
                       <has_line_matching expression="267.4349976 50.7710571289"/>
                       <has_line_matching expression="665.7418213 3.8165459633"/>
-                      <has_line_matching expression="672.2329102 146.2656707764"/>
                       <has_line_matching expression="634.7792969 2367.6374511719"/>
                   </assert_contents>
               </element>