--- a/inspect.xml	Wed Sep 22 21:08:23 2021 +0000
+++ b/inspect.xml	Wed Jul 31 18:07:55 2024 +0000
@@ -1,6 +1,5 @@
-<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_inspect" name="Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description> with scanpy</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
         <xml name="score_genes_params">
@@ -51,6 +50,7 @@
                 label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -66,13 +66,13 @@
     adata=adata,
     expr_type='$method.expr_type',
     var_type='$method.var_type',
-    #if str($method.qc_vars) != ''
+    #if $method.qc_vars
         #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
     qc_vars=$qc_vars,
     #end if
-    #if str($method.percent_top) != ''
+    #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)
 
@@ -125,7 +125,7 @@
     #if str($method.n_pcs) != ''
     n_pcs=$method.n_pcs,
     #end if
-    #if str($method.use_rep) != ''
+    #if $method.use_rep
     use_rep='$method.use_rep',
     #end if
     knn=$method.knn,
@@ -138,7 +138,7 @@
 sc.tl.rank_genes_groups(
     adata=adata,
     groupby='$method.groupby',
-    #if str($method.groups) != ''
+    #if $method.groups
     #set $group=[x.strip() for x in str($method.groups).split(',')]
     groups=$group,
     #end if
@@ -176,13 +176,13 @@
             #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'
     intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
             #end if
-            #if $method.tl_rank_genes_groups_method.solver.random_state
+            #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
     random_state=$method.tl_rank_genes_groups_method.solver.random_state,
             #end if
         #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'
     penalty='l2',
     fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
-            #if $method.tl_rank_genes_groups_method.solver.random_state
+            #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
     random_state=$method.tl_rank_genes_groups_method.solver.random_state,
             #end if
     max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
@@ -213,7 +213,7 @@
 sc.tl.marker_gene_overlap(
     adata,
     reference_markers,
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
     method='$method.overlap.method',
@@ -226,7 +226,7 @@
     #if str($method.adj_pval_threshold) != ''
     adj_pval_threshold=$method.adj_pval_threshold,
     #end if
-    #if str($method.key_added) != ''
+    #if $method.key_added
     key_added='$method.key_added',
     #end if
     inplace=True)
@@ -240,7 +240,7 @@
 sc.pp.scale(
     adata,
     zero_center=$method.zero_center,
-    #if $method.max_value
+    #if str($method.max_value) != ''
     max_value=$method.max_value,
     #end if
     copy=False)
@@ -368,9 +368,9 @@
                 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
                 <conditional name="tl_rank_genes_groups_method">
                     <param argument="method" type="select" label="Method">
-                        <option value="t-test">t-test</option>
+                        <option value="t-test" selected="true">t-test</option>
                         <option value="wilcoxon">Wilcoxon-Rank-Sum</option>
-                        <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option>
+                        <option value="t-test_overestim_var">t-test with overestimate of variance of each group</option>
                         <option value="logreg">Logistic regression</option>
                     </param>
                     <when value="t-test">
@@ -453,7 +453,8 @@
                     </when>
                 </conditional>
             </when>
-            <!--<when value="tl.marker_gene_overlap">
+            <!-- With inplace=True, NotImplementedError: Writing Pandas dataframes to h5ad is currently under development. Please use `inplace=False`. -->
+            <!-- <when value="tl.marker_gene_overlap">
                 <repeat name="reference_markers" title="Marker genes">
                     <param name="key" type="text" value="" label="Cell identity name" help=""/>
                     <param name="values" type="text" value="" label="List of genes" help="Comma-separated names from 'var'"/>
@@ -477,7 +478,7 @@
                 </conditional>
                 <param argument="top_n_markers" type="integer" optional="true" label="Number of top data-derived marker genes to use" help="By default all calculated marker genes are used. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/>
                 <param argument="adj_pval_threshold" type="float" optional="true" label="Significance threshold on the adjusted p-values to select marker genes" help=" This can only be used when adjusted p-values are calculated by 'tl.rank_genes_groups'. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/>
-                <param argument="key_added" type="text" value="" optional="true" label="Key that will contain the marker overlap scores in 'uns'"/>
+                <param argument="key_added" type="text" value="marker_gene_overlap" optional="true" label="Key that will contain the marker overlap scores in 'uns'"/>
             </when>-->
             <when value="pp.log1p"/>
             <when value="pp.scale">
@@ -494,8 +495,8 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-        <test>
-            <!-- test 0 -->
+        <test expect_num_outputs="2">
+            <!-- test 1 -->
             <param name="adata" value="sparce_csr_matrix.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.calculate_qc_metrics"/>
@@ -517,8 +518,8 @@
             </output>
             <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 1 -->
+        <test expect_num_outputs="2">
+            <!-- test 2 -->
             <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.neighbors"/>
@@ -547,8 +548,8 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
-            <!-- test 2 -->
+        <test expect_num_outputs="2">
+            <!-- test 3 -->
             <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.neighbors"/>
@@ -572,8 +573,8 @@
             </output>
             <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 3 -->
+        <test expect_num_outputs="2">
+            <!-- test 4 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.score_genes"/>
@@ -601,8 +602,8 @@
             </output>
             <output name="anndata_out" file="tl.score_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 4 -->
+        <test expect_num_outputs="2">
+            <!-- test 5 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.score_genes_cell_cycle"/>
@@ -633,13 +634,13 @@
             </output>
             <output name="anndata_out" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 5 -->
+        <test expect_num_outputs="2">
+            <!-- test 6 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.rank_genes_groups"/>
                 <param name="groupby" value="cell_type"/>
-                <param name="use_raw" value="True"/>
+                <param name="use_raw" value="False"/>
                 <conditional name="ref">
                     <param name="rest" value="rest"/>
                 </conditional>
@@ -656,7 +657,7 @@
                 <assert_contents>
                     <has_text_matching expression="sc.tl.rank_genes_groups"/>
                     <has_text_matching expression="groupby='cell_type'"/>
-                    <has_text_matching expression="use_raw=True"/>
+                    <has_text_matching expression="use_raw=False"/>
                     <has_text_matching expression="reference='rest'"/>
                     <has_text_matching expression="n_genes=100"/>
                     <has_text_matching expression="method='t-test_overestim_var'"/>
@@ -665,8 +666,8 @@
             </output>
             <output name="anndata_out" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 6 -->
+        <test expect_num_outputs="2">
+            <!-- test 7 -->
             <param name="adata" value="pbmc68k_reduced.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.rank_genes_groups"/>
@@ -714,8 +715,8 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
-            <!-- test 7 -->
+        <test expect_num_outputs="2">
+            <!-- test 8 -->
             <param name="adata" value="pbmc68k_reduced.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.rank_genes_groups"/>
@@ -769,9 +770,9 @@
                 </assert_contents>
             </output>
         </test>
-        <!--<test>
-            < test 9 >
-            <param name="adata" value="tl.rank_genes_groups.louvain.neighbors.pca.pbmc68k_reduced.h5ad" />
+        <!-- test expect_num_outputs="2">
+            < test 9  tl.marker_gene_overlap function was commented because inpace=True does not work>
+            <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.marker_gene_overlap"/>
                 <repeat name="reference_markers">
@@ -787,8 +788,8 @@
                     <param name="value" value="MS4A1"/>
                 </repeat>
                 <conditional name="overlap">
-                    <param argument="method" value="overlap_count"/>
-                    <param argument="normalize" value="None"/>
+                    <param name="method" value="overlap_count"/>
+                    <param name="normalize" value="None"/>
                 </conditional>
             </conditional>
             <assert_stdout>
@@ -796,10 +797,10 @@
                 <has_text_matching expression="key='rank_genes_groups'"/>
                 <has_text_matching expression="method='overlap_count'"/>
             </assert_stdout>
-            <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
-        </test>-->
-        <test>
-            <!-- test 8 -->
+            <output name="anndata_out" file="tl.marker_gene_overlap.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size"/>
+        </test> -->
+        <test expect_num_outputs="2">
+            <!-- test 10 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.log1p"/>
@@ -814,8 +815,8 @@
             </output>
             <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 9 -->
+        <test expect_num_outputs="2">
+            <!-- test 11 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.scale"/>
@@ -832,8 +833,8 @@
             </output>
             <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 10 -->
+        <test expect_num_outputs="2">
+            <!-- test 12 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.scale"/>
@@ -852,8 +853,8 @@
             </output>
             <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 11 -->
+        <test expect_num_outputs="2">
+            <!-- test 13 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.sqrt"/>
@@ -868,6 +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`
@@ -892,7 +917,7 @@
 - pct_dropout_by_{expr_type} (e.g. "pct_dropout_by_counts", percentage of cells this feature does not appear in)
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.calculate_qc_metrics.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__
 
 Compute a neighborhood graph of observations, using `pp.neighbors`
 ==================================================================
@@ -911,7 +936,7 @@
 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.neighbors.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.neighbors.html>`__
 
 Score a set of genes, using `tl.score_genes`
 ============================================
@@ -924,7 +949,7 @@
 for Scanpy by Davide Cittaro.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes.html>`__
 
 Score cell cycle genes, using `tl.score_genes_cell_cycle`
 =========================================================
@@ -934,7 +959,7 @@
 `score_genes` for more explanation.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes_cell_cycle.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__
 
 Rank genes for characterizing groups, using `tl.rank_genes_groups`
 ==================================================================
@@ -950,7 +975,7 @@
 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.rank_genes_groups.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.rank_genes_groups.html>`__
 
 
 Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`)
@@ -963,13 +988,13 @@
 =========================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.log1p.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.log1p.html>`__
 
 Scale data to unit variance and zero mean (`pp.scale`)
 ======================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.scale.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.scale.html>`__
 
 Computes the square root the data matrix (`pp.sqrt`)
 ====================================================