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] 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[]]>