diff normalize.xml @ 6:3bcd5445cd7a draft

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

--- a/normalize.xml	Mon Feb 10 05:28:35 2020 -0500
+++ b/normalize.xml	Thu Feb 20 08:24:54 2020 -0500
@@ -115,13 +115,14 @@
                 <expand macro="param_log"/>
             </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.normalize_total"/>
@@ -132,31 +133,41 @@
                 <param name="layers" value="all"/>
                 <param name="layer_norm" value="None"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.normalize_total"/>
-                <has_text_matching expression="exclude_highly_expressed=False"/>
-                <has_text_matching expression="key_added='n_counts'"/>
-                <has_text_matching expression="layers='all'"/>
-            </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.normalize_total"/>
+                    <has_text_matching expression="exclude_highly_expressed=False"/>
+                    <has_text_matching expression="key_added='n_counts'"/>
+                    <has_text_matching expression="layers='all'"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 2 -->
+            <!-- test 1 -->
             <param name="adata" value="random-randint.h5ad"/>
             <conditional name="method">
                 <param name="method" value="pp.recipe_zheng17"/>
                 <param name="n_top_genes" value="1000"/>
                 <param name="log" value="True"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.recipe_zheng17"/>
-                <has_text_matching expression="n_top_genes=1000"/>
-                <has_text_matching expression="log=True"/>
-            </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.recipe_zheng17"/>
+                    <has_text_matching expression="n_top_genes=1000"/>
+                    <has_text_matching expression="log=True"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 3 -->
+            <!-- test 2 -->
             <param name="adata" value="paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.recipe_weinreb17"/>
@@ -167,31 +178,40 @@
                 <param name="svd_solver" value="randomized"/>
                 <param name="random_state" value="0"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.recipe_weinreb17"/>
-                <has_text_matching expression="log=True"/>
-                <has_text_matching expression="mean_threshold=0.01"/>
-                <has_text_matching expression="cv_threshold=2.0"/>
-                <has_text_matching expression="n_pcs=50"/>
-                <has_text_matching expression="svd_solver='randomized'"/>
-                <has_text_matching expression="random_state=0"/>
-            </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.recipe_weinreb17"/>
+                    <has_text_matching expression="log=True"/>
+                    <has_text_matching expression="mean_threshold=0.01"/>
+                    <has_text_matching expression="cv_threshold=2.0"/>
+                    <has_text_matching expression="n_pcs=50"/>
+                    <has_text_matching expression="svd_solver='randomized'"/>
+                    <has_text_matching expression="random_state=0"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 4 -->
+            <!-- test 3 -->
             <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.recipe_seurat"/>
                 <param name="log" value="True"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.recipe_seurat"/>
-                <has_text_matching expression="log=True"/>
-            </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.recipe_seurat"/>
+                    <has_text_matching expression="log=True"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        
     </tests>
     <help><![CDATA[
 Normalize total counts per cell (`pp.normalize_per_cell`)