diff remove_confounders.xml @ 6:f2f6c703da06 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"

--- a/remove_confounders.xml	Mon Feb 10 05:27:49 2020 -0500
+++ b/remove_confounders.xml	Thu Feb 20 08:24:15 2020 -0500
@@ -103,22 +103,28 @@
                 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/>
             </when>
         </conditional>
+        <expand macro="inputs_common_advanced"/>
     </inputs>
     <outputs>
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
         <test>
-            <!-- test 1 -->
+            <!-- test 0 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.regress_out"/>
                 <param name="keys" value="cell_type"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.regress_out"/>
-                <has_text_matching expression="keys=\['cell_type'\]"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.pp.regress_out"/>
+                    <has_text_matching expression="keys=\['cell_type'\]"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <!--<test>
@@ -135,16 +141,21 @@
             <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>-->
         <test>
-            <!-- test 2 -->
+            <!-- test 1 -->
             <param name="adata" value="blobs.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.combat"/>
                 <param name="key" value="blobs"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.combat"/>
-                <has_text_matching expression="key='blobs'"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.pp.combat"/>
+                    <has_text_matching expression="key='blobs'"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.combat.blobs.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
     </tests>