added output collections

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[]]>