--- a/inspect.xml	Sat May 18 18:33:09 2024 +0000
+++ b/inspect.xml	Wed Jul 31 18:12:22 2024 +0000
@@ -72,7 +72,7 @@
     #end if
     #if $method.percent_top
         #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
-        percent_top=$method.percent_top,
+        percent_top=$percent_top,
     #end if
     inplace=True)
 
@@ -869,6 +869,30 @@
             </output>
             <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
+        <test expect_num_outputs="2">
+            <!-- test 13 -->
+            <param name="adata" value="sparce_csr_matrix.h5ad" />
+            <conditional name="method">
+                <param name="method" value="pp.calculate_qc_metrics"/>
+                <param name="expr_type" value="counts"/>
+                <param name="var_type" value="genes"/>
+                <param name="qc_vars" value="mito,negative"/>
+                <param name="percent_top" value="50,100,200,300"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.pp.calculate_qc_metrics" />
+                    <has_text_matching expression="expr_type='counts'" />
+                    <has_text_matching expression="var_type='genes'" />
+                    <has_text_matching expression="qc_vars=\['mito', 'negative'\]" />
+                    <has_text_matching expression="percent_top=\[50, 100, 200, 300\]" />
+                </assert_contents>
+            </output>
+            <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 Calculate quality control metrics., using `pp.calculate_qc_metrics`