diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml
index a7f21eb7..071dd2bf 100644
--- a/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml
+++ b/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml
@@ -58,7 +58,11 @@
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="batch_key" value="louvain"/>
-      <output name="output_h5" file="combat.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="layers/combat"/>
+        </assert_contents>
+      </output>
     </test>
     <test>
       <param name="input_obj_file" value="find_cluster.h5"/>
diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml
index e7a5e82a..c3857c3a 100644
--- a/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml
+++ b/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml
@@ -114,7 +114,11 @@
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="batch_key" value="louvain"/>
-      <output name="output_h5" file="harmony.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="obsm/X_pca_harmony"/>
+        </assert_contents>
+      </output>
     </test>
     <test>
       <param name="input_obj_file" value="find_cluster.h5"/>
diff --git a/tools/tertiary-analysis/scanpy/scanpy-normalise-data.xml b/tools/tertiary-analysis/scanpy/scanpy-normalise-data.xml
index 390132c3..c495109c 100644
--- a/tools/tertiary-analysis/scanpy/scanpy-normalise-data.xml
+++ b/tools/tertiary-analysis/scanpy/scanpy-normalise-data.xml
@@ -76,6 +76,11 @@ PYTHONIOENCODING=utf-8 scanpy-normalise-data
       <param name="scale_factor" value="1e4"/>
       <param name="save_raw" value="false"/>
       <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="var/n_cells_by_counts"/>
+        </assert_contents>
+      </output>
     </test>
   </tests>
 
diff --git a/tools/tertiary-analysis/scanpy/scanpy-plot-trajectory.xml b/tools/tertiary-analysis/scanpy/scanpy-plot-trajectory.xml
index 37925938..c278e2c0 100644
--- a/tools/tertiary-analysis/scanpy/scanpy-plot-trajectory.xml
+++ b/tools/tertiary-analysis/scanpy/scanpy-plot-trajectory.xml
@@ -100,7 +100,11 @@ PYTHONIOENCODING=utf-8 scanpy-cli plot paga
       <param name="input_obj_file" value="paga.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <output name="output_h5" file="plotted_paga.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="uns/louvain_colors"/>
+        </assert_contents>
+      </output>
       <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
     </test>
   </tests>