updated qcxms

RECETOX · Feb 14, 2024 · da0caf8 · da0caf8
1 parent 7bb3705
commit da0caf8
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Showing 3 changed files with 15 additions and 17 deletions.
diff --git 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
@@ -4,21 +4,22 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+
     <expand macro="edam"/>
     <expand macro="creator"/>
     <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 >> '$log' &&
-        python rename.py
+        /qcxms_bin/qcxms -i molecule.xyz >> '$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
@@ -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[