From 17491b37a5fd439d20ac3f1b29cc6de40fd73948 Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Thu, 11 Mar 2021 14:35:19 +0100
Subject: [PATCH 01/13] PS updated to 2.0.14 SG updated to 4.0.22

---
 tools/peptideshaker/macros_basic.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/peptideshaker/macros_basic.xml b/tools/peptideshaker/macros_basic.xml
index a3aa02edc..7f0c460d6 100755
--- a/tools/peptideshaker/macros_basic.xml
+++ b/tools/peptideshaker/macros_basic.xml
@@ -10,9 +10,9 @@
         </stdio>
     </xml>
     <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
-    <token name="@SEARCHGUI_VERSION@">4.0.12</token>
+    <token name="@SEARCHGUI_VERSION@">4.0.22</token>
     <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
-    <token name="@PEPTIDESHAKER_VERSION@">2.0.9</token>
+    <token name="@PEPTIDESHAKER_VERSION@">2.0.14</token>
     <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
     <xml name="citations">
         <citations>

From 7700dc1cc0f804abf05b47b8be7aca7d2b3f694e Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Sun, 14 Mar 2021 21:25:14 +0100
Subject: [PATCH 02/13] Removed wrong result in test (removed from PS after
 last update).

---
 tools/peptideshaker/peptide_shaker.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 45e567862..3570a5117 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -626,7 +626,6 @@
                       <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>

From a254773c44048708e9ab466de14f174979fda1ec Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Mon, 15 Mar 2021 09:16:59 +0100
Subject: [PATCH 03/13] PS updated to 2.0.15

---
 tools/peptideshaker/macros_basic.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/peptideshaker/macros_basic.xml b/tools/peptideshaker/macros_basic.xml
index 7f0c460d6..4ffd81290 100755
--- a/tools/peptideshaker/macros_basic.xml
+++ b/tools/peptideshaker/macros_basic.xml
@@ -12,7 +12,7 @@
     <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
     <token name="@SEARCHGUI_VERSION@">4.0.22</token>
     <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
-    <token name="@PEPTIDESHAKER_VERSION@">2.0.14</token>
+    <token name="@PEPTIDESHAKER_VERSION@">2.0.15</token>
     <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
     <xml name="citations">
         <citations>

From a9e4f377d9703d77aeda5be151238735bed22f56 Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Mon, 15 Mar 2021 10:05:32 +0100
Subject: [PATCH 04/13] use_shared_home="false"

---
 tools/peptideshaker/peptide_shaker.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 3570a5117..1fb477a32 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -12,8 +12,7 @@
     </requirements>
     <expand macro="stdio" />
 
-    <command><![CDATA[
-    ## When supporting more advanced Galaxy versions:    command use_shared_home="false"
+    <command use_shared_home="false"><![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")

From 93f1d0a2a8c3175adc4b952b416c419907b3c40d Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 12 Mar 2021 21:14:44 +0100
Subject: [PATCH 05/13] some fixes for searchgui and peptideshaker

1. remove stderr redirection

in case of

```
command 2>> $temp_stderr &&
.... &&
cat $temp_stderr 2>&1;
```

stderr is swallowed if command fails.
this was the case for PS, FC, and IP

in case of

```
command 2>> $temp_stderr &&
.... ;
cat $temp_stderr 2>&1;
```

the last cat is executed even if the command fails.
the exit code of the command line is then the exit
code of the cat, i.e. the tool will always be counted
successful, even if everything fails.

2. fix peptideshaker find exec constructs

Galaxy removes the last ';' from the generated command line.
thus we need to make sure that the last `find ... -exec ... \;`
is not the last command.

3. remove some unnecessay parentheses
---
 tools/peptideshaker/fasta_cli.xml      |  6 ++----
 tools/peptideshaker/ident_params.xml   |  8 +-------
 tools/peptideshaker/peptide_shaker.xml | 12 +++++-------
 tools/peptideshaker/searchgui.xml      | 13 +++----------
 4 files changed, 11 insertions(+), 28 deletions(-)

diff --git a/tools/peptideshaker/fasta_cli.xml b/tools/peptideshaker/fasta_cli.xml
index af30c6394..c3082fac5 100755
--- a/tools/peptideshaker/fasta_cli.xml
+++ b/tools/peptideshaker/fasta_cli.xml
@@ -11,7 +11,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set $temp_stderr = "fasta_cli_stderr"
         #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
 
         mkdir output &&
@@ -25,9 +24,8 @@
         ###########################################
 
         echo 'Creating decoy database.' &&
-        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag 2>> $temp_stderr &&
-        mv '${output_db_name}' output &&
-        cat $temp_stderr 2>&1;
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag &&
+        mv '${output_db_name}' output
 ]]>
     </command>
     <inputs>
diff --git a/tools/peptideshaker/ident_params.xml b/tools/peptideshaker/ident_params.xml
index 07e972fb1..b1c2529dd 100755
--- a/tools/peptideshaker/ident_params.xml
+++ b/tools/peptideshaker/ident_params.xml
@@ -12,7 +12,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set $temp_stderr = "searchgui_stderr"
         #set $bin_dir = "bin"
 
         mkdir output;
@@ -20,13 +19,12 @@
         export HOME=\$cwd;
 
 
-        echo "" > $temp_stderr &&
 
         echo 'running Identification Parameters CLI' &&
         #####################################################
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
-        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
+        searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
             --exec_dir="./bin/"
             -out './IdentificationParametersOutput.par'
 
@@ -614,10 +612,6 @@
             #end if
                 -fasta_target_decoy 0
                 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag
-
-        2> $temp_stderr) &&
-
-        cat $temp_stderr 2>&1;
 ]]>
     </command>
     <inputs>
diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 1fb477a32..d11975338 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -16,7 +16,6 @@
         #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
 
@@ -24,8 +23,6 @@
         cwd=`pwd` &&
         export HOME=\$cwd &&
 
-        echo "" > $temp_stderr &&
-
         ln -s '$searchgui_input' searchgui_input.zip &&
 
         ## OPTIONAL MAIN PARAMETERS
@@ -63,7 +60,7 @@
         ######################
         ## 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
@@ -181,8 +178,6 @@
             #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!
@@ -237,6 +232,10 @@
             #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)
@@ -258,7 +257,6 @@
                 && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
             #end if
         #end if
-        && cat $temp_stderr 2>&1;
 ]]>
     </command>
     <inputs>
diff --git a/tools/peptideshaker/searchgui.xml b/tools/peptideshaker/searchgui.xml
index dfbd6006f..f9be0d14b 100755
--- a/tools/peptideshaker/searchgui.xml
+++ b/tools/peptideshaker/searchgui.xml
@@ -17,7 +17,6 @@
         #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;
@@ -27,8 +26,6 @@
         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: ${input_fasta_file.metadata.sequences}';
@@ -59,7 +56,7 @@
         ## Search CLI ##
         ################
         echo 'running search gui' &&
-        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
             -spectrum_files \$cwd
             -fasta_file "\$cwd/input_fasta_file.fasta"
@@ -150,17 +147,13 @@
             ## mgf and database in output
             -output_data 1
 
-        2>> $temp_stderr)
-
         &&
 
-        (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
+        mv output/searchgui_out.zip searchgui_out.zip
 
         &&
 
-        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
-
-        cat $temp_stderr 2>&1;
+        zip -u searchgui_out.zip searchgui.properties
 ]]>
     </command>
     <inputs>

From a6e9a89c5a411fd12f7aae985cc4ddc9d6790925 Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Mon, 15 Mar 2021 11:02:56 +0100
Subject: [PATCH 06/13] Profile updated to 20.01

---
 tools/peptideshaker/peptide_shaker.xml | 9 +++++++--
 tools/peptideshaker/searchgui.xml      | 7 ++++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index d11975338..fd3ab8102 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -1,4 +1,8 @@
-<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>
@@ -11,8 +15,9 @@
         <requirement type="package">unzip</requirement>
     </requirements>
     <expand macro="stdio" />
+    <command use_shared_home="false">
 
-    <command use_shared_home="false"><![CDATA[
+<![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")
diff --git a/tools/peptideshaker/searchgui.xml b/tools/peptideshaker/searchgui.xml
index f9be0d14b..9f55b05c0 100755
--- a/tools/peptideshaker/searchgui.xml
+++ b/tools/peptideshaker/searchgui.xml
@@ -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>
@@ -11,6 +15,7 @@
     </requirements>
     <expand macro="stdio" />
     <command use_shared_home="false">
+      
 <![CDATA[
         #from datetime import datetime
         #import json

From ac361191bbef2813250387afd766e4c0c407ee1b Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Mon, 15 Mar 2021 12:42:57 +0100
Subject: [PATCH 07/13] Added logs to stderr output.

---
 tools/peptideshaker/searchgui.xml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/tools/peptideshaker/searchgui.xml b/tools/peptideshaker/searchgui.xml
index 9f55b05c0..07b865eb5 100755
--- a/tools/peptideshaker/searchgui.xml
+++ b/tools/peptideshaker/searchgui.xml
@@ -15,7 +15,7 @@
     </requirements>
     <expand macro="stdio" />
     <command use_shared_home="false">
-      
+
 <![CDATA[
         #from datetime import datetime
         #import json
@@ -28,6 +28,8 @@
         mkdir output_reports;
         mkdir temp_folder;
         mkdir log_folder;
+        trap ">&2 cat log_folder/*.log" EXIT;
+
         cwd=`pwd`;
         export HOME=\$cwd;
 
@@ -154,6 +156,10 @@
 
         &&
 
+        echo '>log_folder:' &&
+
+        ls -l \$cwd/log_folder &&
+
         mv output/searchgui_out.zip searchgui_out.zip
 
         &&

From d7c905784216bc886fc0777fb1e156f23cd34e95 Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Mon, 15 Mar 2021 12:47:14 +0100
Subject: [PATCH 08/13] Added logs to PS stderr output.

---
 tools/peptideshaker/peptide_shaker.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index fd3ab8102..34b315cd8 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -23,6 +23,7 @@
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $bin_dir = "bin"
         #set $exporting_followup_boolean = False
+        trap ">&2 cat resources/*.log" EXIT;
 
         mkdir output_reports &&
         cwd=`pwd` &&

From 95736b3093e2a93c61f2d183f66af2ea83030b64 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 15 Mar 2021 13:05:10 +0100
Subject: [PATCH 09/13] detect oom errors as fatal_oom and not fatal

---
 tools/peptideshaker/macros_basic.xml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/peptideshaker/macros_basic.xml b/tools/peptideshaker/macros_basic.xml
index 4ffd81290..ae2ded89e 100755
--- a/tools/peptideshaker/macros_basic.xml
+++ b/tools/peptideshaker/macros_basic.xml
@@ -2,10 +2,11 @@
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" level="fatal" description="Job Failed" />
+            <regex match="OutOfMemoryError" level="fatal_oom" description="Out of memory"/>
             <regex match="java.*Exception" level="fatal" description="Java Exception"/>
-            <regex match="Could not reserve enough space for * object heap" level="fatal" description="Out of memory"/>
+            <regex match="Could not reserve enough space for * object heap" level="fatal_oom" description="Out of memory"/>
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
-            <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
+            <regex match="PeptideShaker ran out of memory" level="fatal_oom" description="JVM Error"/>
             <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
     </xml>

From 48797cf750da526e3350796484704a8f3655a9aa Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Mon, 15 Mar 2021 22:18:58 +0100
Subject: [PATCH 10/13] Undone some last features until app behaviour is fixed.

---
 tools/peptideshaker/peptide_shaker.xml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 34b315cd8..3591ef5bd 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -1,8 +1,10 @@
 <tool id="peptide_shaker"
       name="Peptide Shaker"
       version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"
-      profile="20.01"
 >
+<!--  TODO: check trap comment.
+    profile="20.01"
+-->
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -15,15 +17,18 @@
         <requirement type="package">unzip</requirement>
     </requirements>
     <expand macro="stdio" />
+    <!-- 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 $bin_dir = "bin"
         #set $exporting_followup_boolean = False
-        trap ">&2 cat resources/*.log" EXIT;
+        ## 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` &&

From 2bc4ae366f6d4f5335e55e03621e17f48126bfe8 Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Tue, 16 Mar 2021 08:39:46 +0100
Subject: [PATCH 11/13] Refreshing PR

---
 tools/peptideshaker/peptide_shaker.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 3591ef5bd..263ddd167 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -5,6 +5,7 @@
 <!--  TODO: check trap comment.
     profile="20.01"
 -->
+
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>

From bbe7a74e22521fb8d0c395368d3a91ff26955dc8 Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Tue, 16 Mar 2021 12:29:32 +0100
Subject: [PATCH 12/13] Added profile 20.01 to fasta_cli and ident_params tools

---
 tools/peptideshaker/fasta_cli.xml    | 6 +++++-
 tools/peptideshaker/ident_params.xml | 6 +++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/tools/peptideshaker/fasta_cli.xml b/tools/peptideshaker/fasta_cli.xml
index c3082fac5..e3da860cc 100755
--- a/tools/peptideshaker/fasta_cli.xml
+++ b/tools/peptideshaker/fasta_cli.xml
@@ -1,4 +1,8 @@
-<tool id="fasta_cli" name="FastaCLI" version="1.0.1">
+<tool id="fasta_cli"
+      name="FastaCLI"
+      version="1.0.1"
+      profile="20.01"
+>
     <description>
         Appends decoy sequences to FASTA files
     </description>
diff --git a/tools/peptideshaker/ident_params.xml b/tools/peptideshaker/ident_params.xml
index b1c2529dd..6e6accd04 100755
--- a/tools/peptideshaker/ident_params.xml
+++ b/tools/peptideshaker/ident_params.xml
@@ -1,4 +1,8 @@
-<tool id="ident_params" name="Identification Parameters" version="1.5.1">
+<tool id="ident_params"
+      name="Identification Parameters"
+      version="1.5.1"
+      profile="20.01"
+>
     <description>
         Sets the identification parameters to be used in SearchGUI and PeptideShaker apps
     </description>

From f921b219e1e59620f212d9b693e7c74ffdcd78ac Mon Sep 17 00:00:00 2001
From: CarlosHorro <carlos.horro@gmail.com>
Date: Tue, 16 Mar 2021 14:53:20 +0100
Subject: [PATCH 13/13] Readded PS 20.01 profile.

---
 tools/peptideshaker/peptide_shaker.xml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 263ddd167..78aea7f04 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -1,10 +1,8 @@
 <tool id="peptide_shaker"
       name="Peptide Shaker"
       version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"
+      profile="20.01"
 >
-<!--  TODO: check trap comment.
-    profile="20.01"
--->
 
     <description>
         Perform protein identification using various search engines based on results from SearchGUI