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] 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 bd2875864..fc4f5b2ca 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 20137f1c7..0c324d84b 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 be97fcfeb..3cfbe0bc7 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[