--- a/msconvert.xml	Mon Mar 10 07:48:32 2025 +0000
+++ b/msconvert.xml	Fri Apr 25 10:03:36 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="msconvert" name="msconvert" version="@VERSION@.5" profile="@PROFILE_VERSION@">
+<tool id="msconvert" name="msconvert" version="@VERSION@.6" profile="@PROFILE_VERSION@">
     <description>Convert and/or filter mass spectrometry files</description>
     <macros>
         <import>msconvert_macros.xml</import>

--- a/msconvert_macros.xml	Mon Mar 10 07:48:32 2025 +0000
+++ b/msconvert_macros.xml	Fri Apr 25 10:03:36 2025 +0000
@@ -1,7 +1,7 @@
 <macros>
   <token name="@VERSION@">3.0.20287</token>
   <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
-  <token name="@PROFILE_VERSION@">24.2</token>
+  <token name="@PROFILE_VERSION@">23.2</token>
   <xml name="msconvertCommand">
     <command detect_errors="exit_code">
 <![CDATA[
@@ -39,10 +39,12 @@
       ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
     #end if
 
-    CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) &&
-    if [ "\$CAN_SUDO" -eq "0" ]; then
+    ## CAN_SUDO is "" if successful and "1" otherwise
+    CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null || echo \$?) &&
+    echo "CAN SUDO \$CAN_SUDO" &&
+    if [ -z "\$CAN_SUDO" ]; then
       uid=`id -u` &&
-      gid=`id -g` &&    
+      gid=`id -g` &&
       WINE="wine64_anyuser";
     else
       WINE="wine64" &&
@@ -215,14 +217,14 @@
         --outfile '${os.path.splitext($basename)[0]}'
       #end if
       && 
-      if [ "\$CAN_SUDO" -eq "0" ]; then
+      if [ -z "\$CAN_SUDO" ]; then
         sudo chown -R \$uid:\$gid './';
       fi
       #if $general_options.multi_run_output.do_multi_run_output == 'false':
         && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
       #else
         ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
-        ## this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
+        ## this won't be necessay from Galaxy 25.0 https://github.com/galaxyproject/galaxy/pull/19954
         #if $output_type == 'mzML' or $output_type == 'mzXML'
           && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
           ## a newline is needed after `#echo ...` therefore the `;'` on the next line
@@ -430,7 +432,6 @@
 
     </section>
 
-
     <section name="filtering" title="Scan Inclusion/Exclusion Filters">
 
       <param name="activation" type="select" label="Filter by Activation">
@@ -565,7 +566,7 @@
       </data>
       <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection">
         <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter>
-        <discover_datasets pattern="__name_and_ext__" directory="outputs" />
+        <discover_datasets pattern="__name_and_ext__" directory="outputs" sort_by="designation" />
       </collection>
     </outputs>
   </xml>