diff --git a/tools/muon/mudata_import_export.xml b/tools/muon/mudata_import_export.xml
index 7ed36fc599f..13c85eb12de 100644
--- a/tools/muon/mudata_import_export.xml
+++ b/tools/muon/mudata_import_export.xml
@@ -11,21 +11,21 @@
     <configfiles>
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
-#if $method.method == 'import'
+#if $operation.mode == 'import'
 import anndata as ad
 
 mdata = mu.MuData({
-    #for $modality in $method.modalities
+    #for $modality in $operation.modalities
         '$modality.name': ad.read_h5ad('$modality.anndata'),
     #end for
     })
     #if $make_unique
 mdata.var_names_make_unique()
     #end if
-@CMD_mudata_write_outputs@
+mdata.write_h5mu('mudata.h5mu')
 
-#else if $method.method == 'export'
-mdata = mu.read_h5mu('$method.mudata_in')
+#else if $operation.mode == 'export'
+mdata = mu.read_h5mu('$operation.mudata_in')
 for mod in mdata.mod:
     mdata[mod].write_h5ad(mod + '.h5ad')
 
@@ -34,8 +34,8 @@ for mod in mdata.mod:
 ]]></configfile>
     </configfiles>
     <inputs>
-        <conditional name="method">
-            <param name="method" type="select" label="Mode of operation">
+        <conditional name="operation">
+            <param name="mode" type="select" label="Mode of operation">
                 <option value="import" selected="true">Import multiple Anndata objects into a MuData object</option>
                 <option value="export">Export Anndata objects from a MuData objects</option>
             </param>
@@ -58,22 +58,20 @@ for mod in mdata.mod:
         <expand macro="inputs_common_advanced" />
     </inputs>
     <outputs>
-        <expand macro="muon_outputs">
-            <filter>method['method'] == 'import' </filter>
-        </expand>
+        <data name="mudata_out" format="h5ad" from_work_dir="mudata.h5mu" label="MuData object built from ${on_string}">
+            <filter>operation['mode'] == 'import' </filter>
+        </data>
         <collection name="collection_anndata" type="list" label="Anndata objects extracted from ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.*).h5ad" format="h5ad"/>
-            <filter>method['method'] == 'export' </filter>
+            <filter>operation['mode'] == 'export' </filter>
         </collection>
-        <expand macro="outputs_common_advanced">
-            <filter>method['method'] == 'export' </filter>
-        </expand>
+        <expand macro="outputs_common_advanced"/>
     </outputs>
     <tests>
         <test expect_num_outputs="2">
             <!--Import test for RNA and ATAC modalities-->
-            <conditional name="method">
-                <param name="method" value="import"/>
+            <conditional name="operation">
+                <param name="mode" value="import"/>
                 <repeat name="modalities">
                     <param name="name" value="RNA"/>
                     <param name="anndata" location="https://zenodo.org/records/12570984/files/rna.h5ad"/>
@@ -95,10 +93,6 @@ for mod in mdata.mod:
                     <has_text_matching expression="var_names_make_unique()"/>
                 </assert_contents>
             </output>
-            <assert_stdout>
-                <has_text_matching expression="20 × 40"/>
-                <has_text_matching expression="20 x 20"/>
-            </assert_stdout>
             <output name="mudata_out" ftype="h5ad">
                 <assert_contents>
                     <has_h5_keys keys="mod/RNA"/>
@@ -107,10 +101,10 @@ for mod in mdata.mod:
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="2">
             <!--Export test for RNA and ATAC modalities-->
-            <conditional name="method">
-                <param name="method" value="export"/>
+            <conditional name="operation">
+                <param name="mode" value="export"/>
                 <param name="mudata_in" location="https://zenodo.org/records/12570984/files/rna_atac.h5mu"/>
             </conditional>
             <section name="advanced_common">