From 62e7df120c0bb4a4e2ee9d024f498397a73b7735 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Thu, 24 Aug 2023 14:53:39 +0200
Subject: [PATCH 01/20] initial implementation

---
 tools/qcxms/.shed.yml             | 22 +++++++++
 tools/qcxms/macros.xml            | 13 +++++
 tools/qcxms/qcxms_neutral_run.xml | 81 +++++++++++++++++++++++++++++++
 3 files changed, 116 insertions(+)
 create mode 100644 tools/qcxms/.shed.yml
 create mode 100644 tools/qcxms/macros.xml
 create mode 100644 tools/qcxms/qcxms_neutral_run.xml

diff --git a/tools/qcxms/.shed.yml b/tools/qcxms/.shed.yml
new file mode 100644
index 00000000..8da2fe48
--- /dev/null
+++ b/tools/qcxms/.shed.yml
@@ -0,0 +1,22 @@
+name: QCxMS
+owner: recetox
+remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms"
+homepage_url: "https://github.com/grimme-lab/QCxMS"
+categories:
+  - Computational chemistry
+  - Molecular Dynamics
+description: "QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD)."
+long_description: |
+ "QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).
+  It is the successor of the QCEIMS program, in which the EI part is exchanged to x (x=EI, CID) to account for the greater general applicability of the program.
+  The program was originally developed to calculate Electron Ionization (EI) mass spectra, 
+  in which a (typically 70 eV) electron beam is focused on a molecule in order to create an open-shell radical ion (uneven number of valence electrons).
+  This process not only ionizes the molecule, but simultaneously increases the internal energy of the species, which in turn leads to bond breaking, 
+  fragmentation, rearrangement, etc of the ion."
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }} tool from the QCxMS package"
+suite:
+  name: suite_qcxms
+  description: tools from QCxMS are used for molecular geometry optimization and in silico calculation of mass spectra using quantum chemistry
+  type: repository_suite_definition
diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
new file mode 100644
index 00000000..f54745ad
--- /dev/null
+++ b/tools/qcxms/macros.xml
@@ -0,0 +1,13 @@
+<macros>
+    <token name="@TOOL_VERSION@">5.2.0</token>
+
+    <xml name="creator">
+        <creator>
+            <yield/>
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+</macros>
diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
new file mode 100644
index 00000000..3e8edc74
--- /dev/null
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -0,0 +1,81 @@
+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>required as first step to prepare for the production runs</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="creator"/>
+
+    <edam_topics>
+        <edam_topic>topic_3332</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0297</edam_operation>
+    </edam_operations>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        ln $mol molecule.xyz &&
+        cat qcxms.in &&
+        qcxms -i molecule.xyz >> $log
+    ]]></command>
+
+    <environment_variables>
+        <environment_variable name="OMP_NUM_THREADS">1</environment_variable>
+    </environment_variables>
+
+    <configfiles>
+        <configfile filename="qcxms.in"><![CDATA[
+            ${QC_Level}
+            #if $ntraj
+            ntraj  ${keywords.ntraj}
+            #end if
+            tmax  ${keywords.tmax} 
+            tinit  ${keywords.tinit} 
+            ieeatm  ${keywords.ieeatm}]]>
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param type="data" name="Molecule 3D structure [.xzy]" format="xyz" />
+        <param name="QC_Level" type="select" display="radio" label="QC Method">
+            <option value="xtb2" selected="true">GFN2-xTB</option>
+            <option value="xtb">GFN-xTB</option>
+        </param>
+        <section name="keywords" title="Advanced method parameters" expanded="false" 
+            help="List of advanced keywords to specify the method - for more information see [1].">
+            <param name="tmax" type="float" value="20.0" label="Maximum MD time (sampling) [ps]"
+            help="MD time for the mean-free-path (mfp) simulation in the EI mode. In the CID mode, this sets the number of time steps for the simulation 
+            after fragmentation during internal energy scaling (implicit run type). For the explicit run type, the time for the collision MDs is fixed at 50 fs * number_of_atoms."/>
+            <param name="tinit" type="float" value="500.0" label="Initial Temperature [K]"/>
+            <param name="ieeatm" type="float" value="0.6" label="Impact excess energy (IEE) per atom [eV/atom]" />
+            <param name="ntraj" type="integer" optional="true" min="1" label="Number of trajectories[#]" help="Default is 25 * no. of atoms if unspecified."/>
+        </section>
+        <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs?" help="Output the logfile and generated trajectory."/>
+    </inputs>
+
+    <outputs>
+        <data name="qcxms_out" format="gs" from_work_dir="qcxms.gs" label="qcxms.gs generated by ${tool.name} on ${on_string}" />
+        <data name="trajectory" from_work_dir="trjM" format="txt" label="trajectories generated by ${tool.name} on ${on_string}">
+            <filter>store_extended_output</filter>
+        </data>
+        <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}">
+            <filter>store_extended_output</filter>
+        </data>
+    </outputs>
+
+    <help><![CDATA[]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1002/anie.201300158</citation>
+        <citation type="doi">10.1039/C4OB01668H</citation>
+        <citation type="doi">10.1021/jp5096618</citation>
+        <citation type="doi">10.1255/ejms.1313</citation>
+        <citation type="doi">10.1021/acs.jpca.6b02907</citation>
+    </citations>
+</tool>
\ No newline at end of file

From acf0b9675364b0d3763a042e0ef3e299107dac06 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 11 Sep 2023 16:12:41 +0200
Subject: [PATCH 02/20] added check for number of trajectories

---
 tools/qcxms/qcxms_neutral_run.xml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 3e8edc74..5de6a122 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -21,6 +21,7 @@
     <command detect_errors="exit_code"><![CDATA[
         ln $mol molecule.xyz &&
         cat qcxms.in &&
+        qcxms -i molecule.xyz >> $log &&
         qcxms -i molecule.xyz >> $log
     ]]></command>
 
@@ -31,7 +32,7 @@
     <configfiles>
         <configfile filename="qcxms.in"><![CDATA[
             ${QC_Level}
-            #if $ntraj
+            #if $keywords.ntraj
             ntraj  ${keywords.ntraj}
             #end if
             tmax  ${keywords.tmax} 
@@ -41,7 +42,7 @@
     </configfiles>
 
     <inputs>
-        <param type="data" name="Molecule 3D structure [.xzy]" format="xyz" />
+        <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" />
         <param name="QC_Level" type="select" display="radio" label="QC Method">
             <option value="xtb2" selected="true">GFN2-xTB</option>
             <option value="xtb">GFN-xTB</option>
@@ -59,13 +60,21 @@
     </inputs>
 
     <outputs>
-        <data name="qcxms_out" format="gs" from_work_dir="qcxms.gs" label="qcxms.gs generated by ${tool.name} on ${on_string}" />
+        <data name="qcxms_out" format="txt" from_work_dir="qcxms.gs" label="qcxms.gs generated by ${tool.name} on ${on_string}">
+            <filter>store_extended_output</filter>
+        </data>
         <data name="trajectory" from_work_dir="trjM" format="txt" label="trajectories generated by ${tool.name} on ${on_string}">
             <filter>store_extended_output</filter>
         </data>
         <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}">
             <filter>store_extended_output</filter>
         </data>
+
+
+        <collection name="coords" type="list">
+            <discover_datasets pattern="__designation_and_ext__" format="xyz" directory="TMPQCXMS" recurse="true"/>
+        </collection>
+
     </outputs>
 
     <help><![CDATA[]]>

From b41fe7c0e4b9f93a3aa090898bef6f3a7e0d36cb Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 26 Sep 2023 14:33:46 +0200
Subject: [PATCH 03/20] added test data

---
 tools/qcxms/test-data/mol.xyz | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 tools/qcxms/test-data/mol.xyz

diff --git a/tools/qcxms/test-data/mol.xyz b/tools/qcxms/test-data/mol.xyz
new file mode 100644
index 00000000..92335cf7
--- /dev/null
+++ b/tools/qcxms/test-data/mol.xyz
@@ -0,0 +1,20 @@
+18
+Lindane
+CL     -2.3574740887    0.2795224786    1.4453580379
+C      -1.5060254335   -0.0564753152   -0.1808833480
+C      -0.7409992814    1.1908990145   -0.6060928106
+C      -0.6154388189   -1.2913844585   -0.1359211653
+CL     -0.4997346103    1.0723730326   -2.4801609516
+C       0.6426193118    1.3751488924    0.0051864041
+CL     -1.5938731432   -2.7512128353    0.4462303221
+C       0.6645445824   -1.0841370821    0.6675278544
+CL      0.4618762434    2.1580321789    1.6895099878
+C       1.4344482422    0.0744384378    0.0415960811
+CL      1.6999230385   -2.6236054897    0.5561774969
+CL      3.0750505924    0.3596521318    0.8505522013
+H      -2.3252866268   -0.2277424186   -0.8540474772
+H      -1.3395941257    2.0737268925   -0.4863004684
+H      -0.3587814867   -1.5482350588   -1.1510624886
+H       1.1898183823    2.1143426895   -0.5496439934
+H       0.4745289683   -0.9351251125    1.7152343988
+H       1.6943985224   -0.1802178770   -0.9732601047

From fcc97d6cb3b339b3f45b3292f5be48a04d142107 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Thu, 5 Oct 2023 18:51:24 +0200
Subject: [PATCH 04/20] added output collections

---
 tools/qcxms/qcxms_neutral_run.xml | 37 ++++++++++++++++++++++++++-----
 1 file changed, 32 insertions(+), 5 deletions(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 5de6a122..be598e11 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -22,7 +22,9 @@
         ln $mol molecule.xyz &&
         cat qcxms.in &&
         qcxms -i molecule.xyz >> $log &&
-        qcxms -i molecule.xyz >> $log
+        qcxms -i molecule.xyz >> $log &&
+        python3 rename.py
+
     ]]></command>
 
     <environment_variables>
@@ -39,6 +41,27 @@
             tinit  ${keywords.tinit} 
             ieeatm  ${keywords.ieeatm}]]>
         </configfile>
+        <configfile filename="rename.py">
+import os
+
+def rename_files_with_folder_name(folder_path):
+    if not os.path.exists(folder_path):
+        print(f"The folder '{folder_path}' does not exist.")
+        return
+
+    for root, _, files in os.walk(folder_path):
+        for filename in files:
+            folder_name = os.path.basename(root)
+            new_filename = f"{folder_name}_{filename}"
+            
+            old_path = os.path.join(root, filename)
+            new_path = os.path.join(root, new_filename)
+
+            os.rename(old_path, new_path)
+
+path = os.getcwd() + "/TMPQCXMS"
+rename_files_with_folder_name(path) 
+        </configfile>
     </configfiles>
 
     <inputs>
@@ -70,11 +93,15 @@
             <filter>store_extended_output</filter>
         </data>
 
-
-        <collection name="coords" type="list">
-            <discover_datasets pattern="__designation_and_ext__" format="xyz" directory="TMPQCXMS" recurse="true"/>
+        <collection name="coords1" type="list" label="coords in files generated by ${tool.name} on ${on_string}" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.in" ext="in" directory="TMPQCXMS" recurse="true"/>
+        </collection>
+        <collection name="coords2" type="list" label="coords start files generated by ${tool.name} on ${on_string}" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.start" ext="start" directory="TMPQCXMS" recurse="true"/>
+        </collection>
+        <collection name="coords3" format="xyz" type="list" label="coords xyz files generated by ${tool.name} on ${on_string}" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xyz" format="xyz" ext="xyz" directory="TMPQCXMS" recurse="true"/>
         </collection>
-
     </outputs>
 
     <help><![CDATA[]]>

From 02184ad56a3b25b4770bc589fcce3c41983e115b Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Fri, 20 Oct 2023 16:55:22 +0200
Subject: [PATCH 05/20] added test for qcxms_neutral_run

---
 tools/qcxms/qcxms_neutral_run.xml | 38 +++++++++++++++++++++++++++----
 1 file changed, 33 insertions(+), 5 deletions(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index be598e11..b652b724 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -77,7 +77,7 @@ rename_files_with_folder_name(path)
             after fragmentation during internal energy scaling (implicit run type). For the explicit run type, the time for the collision MDs is fixed at 50 fs * number_of_atoms."/>
             <param name="tinit" type="float" value="500.0" label="Initial Temperature [K]"/>
             <param name="ieeatm" type="float" value="0.6" label="Impact excess energy (IEE) per atom [eV/atom]" />
-            <param name="ntraj" type="integer" optional="true" min="1" label="Number of trajectories[#]" help="Default is 25 * no. of atoms if unspecified."/>
+            <param name="ntraj" type="integer" optional="true" min="2" label="Number of trajectories[#]" help="Default is 25 * no. of atoms if unspecified."/>
         </section>
         <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs?" help="Output the logfile and generated trajectory."/>
     </inputs>
@@ -93,17 +93,45 @@ rename_files_with_folder_name(path)
             <filter>store_extended_output</filter>
         </data>
 
-        <collection name="coords1" type="list" label="coords in files generated by ${tool.name} on ${on_string}" >
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.in" ext="in" directory="TMPQCXMS" recurse="true"/>
+        <collection name="coords1" format="txt" type="list" label="coords in files generated by ${tool.name} on ${on_string}" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.in" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
-        <collection name="coords2" type="list" label="coords start files generated by ${tool.name} on ${on_string}" >
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.start" ext="start" directory="TMPQCXMS" recurse="true"/>
+        <collection name="coords2" format="txt" type="list" label="coords start files generated by ${tool.name} on ${on_string}" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.start" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
         <collection name="coords3" format="xyz" type="list" label="coords xyz files generated by ${tool.name} on ${on_string}" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xyz" format="xyz" ext="xyz" directory="TMPQCXMS" recurse="true"/>
         </collection>
     </outputs>
 
+    <tests>
+        <test expect_num_outputs="6">
+            <param name="mol" value="mol.xyz" ftype="xyz"/>
+            <section name="keywords">
+                <param name="ntraj" value="2"/>
+            </section>
+            <param name="store_extended_output" value="true"/>
+            <output_collection name="coords1" type="list" count="2"/>
+            <output_collection name="coords2" type="list" count="2"/>
+            <output_collection name="coords3" type="list" count="2"/>
+            <output name="qcxms_out">
+                <assert_contents>
+                    <has_size value="174613" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="trajectory">
+                <assert_contents>
+                    <has_size value="22150" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="log">
+                <assert_contents>
+                    <has_size value="10518" delta="300"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
     <help><![CDATA[]]>
     </help>
 

From f6441e9244b886ee783457a7709dbed4a9883f65 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Fri, 20 Oct 2023 16:56:14 +0200
Subject: [PATCH 06/20] added qcxms_prod_run

---
 tools/qcxms/qcxms_prod_run.xml | 90 ++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 tools/qcxms/qcxms_prod_run.xml

diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
new file mode 100644
index 00000000..9af7f601
--- /dev/null
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -0,0 +1,90 @@
+<tool id="qcxms_prod_run" name="QCxMS prod run" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>production runs</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="creator"/>
+
+    <edam_topics>
+        <edam_topic>topic_3332</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0297</edam_operation>
+    </edam_operations>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python3 ${create_folder} &&
+        find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && qcxms --prod >> $log' &&
+        getres &&
+        plotms
+    ]]></command>
+
+    <environment_variables>
+        <environment_variable name="OMP_NUM_THREADS">1</environment_variable>
+    </environment_variables>
+
+    <configfiles>
+        <configfile name="create_folder">
+import os
+import shutil
+
+#set folder1_files = str("', '").join([str($f) for $f in $in_files])
+#set folder2_files = str("', '").join([str($f) for $f in $start_files])
+#set folder3_files = str("', '").join([str($f) for $f in $xyz_files])
+
+#set names = str("', '").join([str($f.name) for $f in $xyz_files])
+names = '$names'
+folder_names = [x.split("_")[0] for x in names]
+
+folder1_files = '$folder1_files'
+folder2_files = '$folder2_files'
+folder3_files = '$folder3_files'
+
+# Create a new output folder to store the result
+output_path = 'TMPQCXMS'
+os.makedirs(output_path, exist_ok=True)
+
+for fname, filename1, filename2, filename3 in zip(folder_names, folder1_files, folder2_files, folder3_files):
+    new_folder_path = os.path.join(output_path, fname)
+    os.makedirs(new_folder_path, exist_ok=True)
+
+    shutil.copy2(os.path.join(os.path.dirname(folder1_files[0]), filename1), os.path.join(new_folder_path, 'qcxms.in'))
+    shutil.copy2(os.path.join(os.path.dirname(folder2_files[0]), filename2), os.path.join(new_folder_path, 'qcxms.start'))
+    shutil.copy2(os.path.join(os.path.dirname(folder3_files[0]), filename3), os.path.join(new_folder_path, 'start.xyz'))
+
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param type="data_collection" collection_type="list" name="in_files" label="in files [.in]" format="in,txt,text"/>
+        <param type="data_collection" collection_type="list" name="start_files" label="start files [.start]" format="start,txt,text"/>
+        <param type="data_collection" collection_type="list" name="xyz_files" label="xyz files [.xyz]" format="xyz,txt,text"/>
+    </inputs>
+
+    <outputs>
+        <data name="result" format="txt" from_work_dir="result.jdx" label="results.jdx generated by ${tool.name} on ${on_string}"/>
+
+        <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test expect_failure="true" />
+    </tests>
+
+    <help><![CDATA[]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1002/anie.201300158</citation>
+        <citation type="doi">10.1039/C4OB01668H</citation>
+        <citation type="doi">10.1021/jp5096618</citation>
+        <citation type="doi">10.1255/ejms.1313</citation>
+        <citation type="doi">10.1021/acs.jpca.6b02907</citation>
+    </citations>
+</tool>
\ No newline at end of file

From 3a753b27298f8a45389c5ee14899eeee092bb784 Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Sat, 21 Oct 2023 12:18:28 +0000
Subject: [PATCH 07/20] Update tools/qcxms/qcxms_neutral_run.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/qcxms/qcxms_neutral_run.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index b652b724..72317542 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy0" profile="21.05">
     <description>required as first step to prepare for the production runs</description>
     
     <macros>

From cf0a816b065a4246837a4a1ba6ec55683d3a5e35 Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Sat, 21 Oct 2023 12:18:43 +0000
Subject: [PATCH 08/20] Update tools/qcxms/qcxms_neutral_run.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/qcxms/qcxms_neutral_run.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 72317542..9d4115a0 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -21,8 +21,8 @@
     <command detect_errors="exit_code"><![CDATA[
         ln $mol molecule.xyz &&
         cat qcxms.in &&
-        qcxms -i molecule.xyz >> $log &&
-        qcxms -i molecule.xyz >> $log &&
+        qcxms -i molecule.xyz >> '$log' &&
+        qcxms -i molecule.xyz >> '$log' &&
         python3 rename.py
 
     ]]></command>

From f7b32ed064d3211f8593d6293a8164072964424a Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Sat, 21 Oct 2023 12:18:55 +0000
Subject: [PATCH 09/20] Update tools/qcxms/qcxms_neutral_run.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/qcxms/qcxms_neutral_run.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 9d4115a0..19f81ef4 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -19,7 +19,7 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        ln $mol molecule.xyz &&
+        ln -s '$mol' molecule.xyz &&
         cat qcxms.in &&
         qcxms -i molecule.xyz >> '$log' &&
         qcxms -i molecule.xyz >> '$log' &&

From bfcbeb9b8d949a8a8ccb4db0b041f01b7bb6346d Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Sat, 21 Oct 2023 12:19:04 +0000
Subject: [PATCH 10/20] Update tools/qcxms/qcxms_prod_run.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/qcxms/qcxms_prod_run.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index 9af7f601..53afbed9 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -19,7 +19,7 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        python3 ${create_folder} &&
+        python3 '${create_folder}' &&
         find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && qcxms --prod >> $log' &&
         getres &&
         plotms

From afa7e6a3703eaee560d9bfcc88909a91aa2c6241 Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Sat, 21 Oct 2023 12:19:24 +0000
Subject: [PATCH 11/20] Update tools/qcxms/qcxms_prod_run.xml

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

diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index 53afbed9..ce823aeb 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_prod_run" name="QCxMS prod run" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy0" profile="21.05">
     <description>production runs</description>
     
     <macros>

From 77886de66a13a179bbbb88bbd5ade5689683dadb Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 23 Oct 2023 12:08:31 +0200
Subject: [PATCH 12/20] fixed issues

---
 tools/qcxms/macros.xml            | 14 +++++++++++
 tools/qcxms/qcxms_neutral_run.xml | 16 +++----------
 tools/qcxms/qcxms_prod_run.xml    | 40 ++++++++++++-------------------
 3 files changed, 32 insertions(+), 38 deletions(-)

diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
index f54745ad..37fb2a8f 100644
--- a/tools/qcxms/macros.xml
+++ b/tools/qcxms/macros.xml
@@ -1,5 +1,19 @@
 <macros>
     <token name="@TOOL_VERSION@">5.2.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
+            <requirement type="package" version="3.8">python</requirement>
+        </requirements>
+    </xml>
+    <xml name="edam">
+        <edam_topics>
+            <edam_topic>topic_3332</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0297</edam_operation>
+        </edam_operations>
+    </xml>
 
     <xml name="creator">
         <creator>
diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 19f81ef4..10d4a56e 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -4,26 +4,16 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-
+    <expand macro="edam"/>
     <expand macro="creator"/>
-
-    <edam_topics>
-        <edam_topic>topic_3332</edam_topic>
-    </edam_topics>
-    <edam_operations>
-        <edam_operation>operation_0297</edam_operation>
-    </edam_operations>
-
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
-    </requirements>
+    <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$mol' molecule.xyz &&
         cat qcxms.in &&
         qcxms -i molecule.xyz >> '$log' &&
         qcxms -i molecule.xyz >> '$log' &&
-        python3 rename.py
+        python rename.py
 
     ]]></command>
 
diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index ce823aeb..d3b8a31c 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -1,25 +1,15 @@
 <tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy0" profile="21.05">
-    <description>production runs</description>
+    <description>Production run to obtain a QCxMS simulated mass spectrum</description>
     
     <macros>
         <import>macros.xml</import>
     </macros>
-
+    <expand macro="edam"/>
     <expand macro="creator"/>
-
-    <edam_topics>
-        <edam_topic>topic_3332</edam_topic>
-    </edam_topics>
-    <edam_operations>
-        <edam_operation>operation_0297</edam_operation>
-    </edam_operations>
-
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
-    </requirements>
+    <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-        python3 '${create_folder}' &&
+        python '${create_folder}' &&
         find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && qcxms --prod >> $log' &&
         getres &&
         plotms
@@ -34,29 +24,29 @@
 import os
 import shutil
 
-#set folder1_files = str("', '").join([str($f) for $f in $in_files])
-#set folder2_files = str("', '").join([str($f) for $f in $start_files])
-#set folder3_files = str("', '").join([str($f) for $f in $xyz_files])
+#set in_collection = str("', '").join([str($f) for $f in $in_files])
+#set start_collection = str("', '").join([str($f) for $f in $start_files])
+#set xyz_collection = str("', '").join([str($f) for $f in $xyz_files])
 
 #set names = str("', '").join([str($f.name) for $f in $xyz_files])
 names = '$names'
 folder_names = [x.split("_")[0] for x in names]
 
-folder1_files = '$folder1_files'
-folder2_files = '$folder2_files'
-folder3_files = '$folder3_files'
+in_collection = '$in_collection'
+start_collection = '$start_collection'
+xyz_collection = '$xyz_collection'
 
 # Create a new output folder to store the result
 output_path = 'TMPQCXMS'
 os.makedirs(output_path, exist_ok=True)
 
-for fname, filename1, filename2, filename3 in zip(folder_names, folder1_files, folder2_files, folder3_files):
-    new_folder_path = os.path.join(output_path, fname)
+for folder_name, in_file, start_file, xyz_file in zip(folder_names, in_collection, start_collection, xyz_collection):
+    new_folder_path = os.path.join(output_path, folder_name)
     os.makedirs(new_folder_path, exist_ok=True)
 
-    shutil.copy2(os.path.join(os.path.dirname(folder1_files[0]), filename1), os.path.join(new_folder_path, 'qcxms.in'))
-    shutil.copy2(os.path.join(os.path.dirname(folder2_files[0]), filename2), os.path.join(new_folder_path, 'qcxms.start'))
-    shutil.copy2(os.path.join(os.path.dirname(folder3_files[0]), filename3), os.path.join(new_folder_path, 'start.xyz'))
+    shutil.copy2(os.path.join(os.path.dirname(in_collection[0]), in_file), os.path.join(new_folder_path, 'qcxms.in'))
+    shutil.copy2(os.path.join(os.path.dirname(start_collection[0]), start_file), os.path.join(new_folder_path, 'qcxms.start'))
+    shutil.copy2(os.path.join(os.path.dirname(xyz_collection[0]), xyz_file), os.path.join(new_folder_path, 'start.xyz'))
 
         </configfile>
     </configfiles>

From 3b801403134fe40cf8b142d92a4ebf8953c45a0a Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 23 Oct 2023 16:17:15 +0200
Subject: [PATCH 13/20] updated qcxms_neutral_run

---
 tools/qcxms/qcxms_neutral_run.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 10d4a56e..20137f1c 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -122,7 +122,11 @@ rename_files_with_folder_name(path)
         </test>
     </tests>
 
-    <help><![CDATA[]]>
+    <help><![CDATA[
+        The QCxMS Neutral Run tool serves as the first step in preparing for production runs. The tool execute neutral runs for mass 
+        spectrometry simulations using the GFN2-xTB and GFN-xTB quantum chemistry methods. For detail information visit the documentation 
+        at https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_run.html#excecuting-the-production-runs
+        ]]>
     </help>
 
     <citations>

From bc5f15331788dacd0de6a7b45fe15db0c8b66000 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 23 Oct 2023 17:06:48 +0200
Subject: [PATCH 14/20] updated qcxms_production_run

---
 tools/qcxms/qcxms_prod_run.xml | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index d3b8a31c..be97fcfe 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -9,10 +9,11 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-        python '${create_folder}' &&
+        python '${create_folder_structure}' &&
         find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && qcxms --prod >> $log' &&
         getres &&
-        plotms
+        plotms &&
+        sh ${__tool_directory__}/msp_out.sh
     ]]></command>
 
     <environment_variables>
@@ -20,7 +21,7 @@
     </environment_variables>
 
     <configfiles>
-        <configfile name="create_folder">
+        <configfile name="create_folder_structure">
 import os
 import shutil
 
@@ -55,19 +56,25 @@ for folder_name, in_file, start_file, xyz_file in zip(folder_names, in_collectio
         <param type="data_collection" collection_type="list" name="in_files" label="in files [.in]" format="in,txt,text"/>
         <param type="data_collection" collection_type="list" name="start_files" label="start files [.start]" format="start,txt,text"/>
         <param type="data_collection" collection_type="list" name="xyz_files" label="xyz files [.xyz]" format="xyz,txt,text"/>
+        <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs" help="Output the logfile."/>
     </inputs>
 
     <outputs>
-        <data name="result" format="txt" from_work_dir="result.jdx" label="results.jdx generated by ${tool.name} on ${on_string}"/>
-
-        <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}"/>
+        <data name="msp_output" format="msp" from_work_dir="simulated_spectra.msp" label="simulated_spectra.msp generated by ${tool.name} on ${on_string}"/>
+        <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}">
+            <filter>store_extended_output</filter>
+        </data>
     </outputs>
 
     <tests>
         <test expect_failure="true" />
     </tests>
 
-    <help><![CDATA[]]>
+    <help><![CDATA[
+        The QCxMS production run tool is used to simulate mass spectra for a given molecule using the QCxMS (Quantum Chemistry by Mass Spectrometry) method. 
+        This tool generates simulated mass spectra based on the equilibrium structure of a molecule and allows you to perform QCxMS production runs.
+        For detail information visit the documentation at https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_run.html#excecuting-the-production-runs
+        ]]>
     </help>
 
     <citations>

From e463b3452e2158c62dc67f03bb50319ee542bd2b Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 23 Oct 2023 17:07:06 +0200
Subject: [PATCH 15/20] added msp_out.sh

---
 tools/qcxms/msp_out.sh | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 tools/qcxms/msp_out.sh

diff --git a/tools/qcxms/msp_out.sh b/tools/qcxms/msp_out.sh
new file mode 100644
index 00000000..09fc9361
--- /dev/null
+++ b/tools/qcxms/msp_out.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+molname=`sed -n '2{p;q}'  TMPQCXMS/TMP.1/start.xyz`
+kword=$(grep 'NPOINTS' result.jdx)
+num_peaks=$(echo "$kword" | sed 's/^[^=]*=//')
+echo `pwd`
+sed -n '/PEAK/,/END/{/PEAK/!{/END/!p}}' result.jdx > temp.dat
+awk '{print $1, $2}' temp.dat > tempa.dat
+sed "1s/^/NAME: $molname\nNum Peaks: $num_peaks\n/" tempa.dat >> simulated_spectra.msp
+sed -i '$a\ ' simulated_spectra.msp
+rm temp.dat tempa.dat
\ No newline at end of file

From 9ce9dba36eb0000c8d77763af3919dc64a0c14d4 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Fri, 27 Oct 2023 16:50:01 +0200
Subject: [PATCH 16/20] added plotms as requirement

---
 tools/qcxms/macros.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
index 37fb2a8f..df8fe3dc 100644
--- a/tools/qcxms/macros.xml
+++ b/tools/qcxms/macros.xml
@@ -3,6 +3,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
+            <requirement type="package" version="6.2.0">plotms</requirement>
             <requirement type="package" version="3.8">python</requirement>
         </requirements>
     </xml>

From 7bb3705881d0ffc9c0bab794e58d55c94314f0e3 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 30 Oct 2023 17:30:23 +0100
Subject: [PATCH 17/20] updated qcxms version to 5.2.1

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

diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
index df8fe3dc..bd287586 100644
--- a/tools/qcxms/macros.xml
+++ b/tools/qcxms/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">5.2.0</token>
+    <token name="@TOOL_VERSION@">5.2.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>

From da0caf88efecd148620fd40a797c652df670ae29 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Wed, 14 Feb 2024 17:05:33 +0100
Subject: [PATCH 18/20] updated qcxms

---
 tools/qcxms/macros.xml            |  4 +---
 tools/qcxms/qcxms_neutral_run.xml | 17 +++++++++--------
 tools/qcxms/qcxms_prod_run.xml    | 11 +++++------
 3 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
index bd287586..fc4f5b2c 100644
--- a/tools/qcxms/macros.xml
+++ b/tools/qcxms/macros.xml
@@ -2,9 +2,7 @@
     <token name="@TOOL_VERSION@">5.2.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">qcxms</requirement>
-            <requirement type="package" version="6.2.0">plotms</requirement>
-            <requirement type="package" version="3.8">python</requirement>
+            <container type="docker">recetox/qcxms-docker:@TOOL_VERSION@</container>
         </requirements>
     </xml>
     <xml name="edam">
diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 20137f1c..0c324d84 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -4,6 +4,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    
     <expand macro="edam"/>
     <expand macro="creator"/>
     <expand macro="requirements"/>
@@ -11,14 +12,14 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$mol' molecule.xyz &&
         cat qcxms.in &&
-        qcxms -i molecule.xyz >> '$log' &&
-        qcxms -i molecule.xyz >> '$log' &&
-        python rename.py
+        /qcxms_bin/qcxms -i molecule.xyz >> '$log' &&
+        /qcxms_bin/qcxms -i molecule.xyz >> '$log' &&
+        python3 rename.py
 
     ]]></command>
 
     <environment_variables>
-        <environment_variable name="OMP_NUM_THREADS">1</environment_variable>
+        <environment_variable name="OMP_NUM_THREADS">1,2,1</environment_variable>
     </environment_variables>
 
     <configfiles>
@@ -55,7 +56,7 @@ rename_files_with_folder_name(path)
     </configfiles>
 
     <inputs>
-        <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" />
+        <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz,txt" />
         <param name="QC_Level" type="select" display="radio" label="QC Method">
             <option value="xtb2" selected="true">GFN2-xTB</option>
             <option value="xtb">GFN-xTB</option>
@@ -89,14 +90,14 @@ rename_files_with_folder_name(path)
         <collection name="coords2" format="txt" type="list" label="coords start files generated by ${tool.name} on ${on_string}" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.start" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
-        <collection name="coords3" format="xyz" type="list" label="coords xyz files generated by ${tool.name} on ${on_string}" >
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xyz" format="xyz" ext="xyz" directory="TMPQCXMS" recurse="true"/>
+        <collection name="coords3" format="txt" type="list" label="coords xyz files generated by ${tool.name} on ${on_string}" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xyz" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
     </outputs>
 
     <tests>
         <test expect_num_outputs="6">
-            <param name="mol" value="mol.xyz" ftype="xyz"/>
+            <param name="mol" value="mol.xyz" ftype="txt"/>
             <section name="keywords">
                 <param name="ntraj" value="2"/>
             </section>
diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index be97fcfe..3cfbe0bc 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -9,15 +9,15 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-        python '${create_folder_structure}' &&
-        find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && qcxms --prod >> $log' &&
-        getres &&
-        plotms &&
+        python3 '${create_folder_structure}' &&
+        find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && /qcxms_bin/qcxms --prod >> $log' &&
+        /qcxms_bin/getres &&
+        /plotms_bin/PlotMS.v.6.2.0/plotms &&
         sh ${__tool_directory__}/msp_out.sh
     ]]></command>
 
     <environment_variables>
-        <environment_variable name="OMP_NUM_THREADS">1</environment_variable>
+        <environment_variable name="OMP_NUM_THREADS">1,2,1</environment_variable>
     </environment_variables>
 
     <configfiles>
@@ -67,7 +67,6 @@ for folder_name, in_file, start_file, xyz_file in zip(folder_names, in_collectio
     </outputs>
 
     <tests>
-        <test expect_failure="true" />
     </tests>
 
     <help><![CDATA[

From 5437ced8c6fe146c6b3afa80f4315d8dfe482690 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <46793118+zargham-ahmad@users.noreply.github.com>
Date: Thu, 15 Feb 2024 15:37:13 +0100
Subject: [PATCH 19/20] Update tools/qcxms/qcxms_prod_run.xml

Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
---
 tools/qcxms/qcxms_prod_run.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index 3cfbe0bc..7bb19149 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -67,6 +67,7 @@ for folder_name, in_file, start_file, xyz_file in zip(folder_names, in_collectio
     </outputs>
 
     <tests>
+        <test expect_failure="true"/>
     </tests>
 
     <help><![CDATA[

From dda00b3493e6f544e641379c11825872197cf057 Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Thu, 15 Feb 2024 14:52:24 +0000
Subject: [PATCH 20/20] Update tools/qcxms/qcxms_prod_run.xml

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

diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index 7bb19149..3501bcd2 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -10,7 +10,7 @@
 
     <command detect_errors="exit_code"><![CDATA[
         python3 '${create_folder_structure}' &&
-        find TMPQCXMS/*/ -type d | xargs -I {} -P 4 sh -c 'cd {} && /qcxms_bin/qcxms --prod >> $log' &&
+        find TMPQCXMS/*/ -type d | xargs -I {} -P ${GALAXY_SLOTS} sh -c 'cd {} && /qcxms_bin/qcxms --prod >> $log' &&
         /qcxms_bin/getres &&
         /plotms_bin/PlotMS.v.6.2.0/plotms &&
         sh ${__tool_directory__}/msp_out.sh