comparison plot.xml @ 6:dbbe1ea8ecb1 draft

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

5:8599fd07d140

    groupby='$method.groupby',
    #end if
    log=$method.log,
    use_raw=$method.use_raw,
    @CMD_conditional_stripplot@
    multi_panel=$method.violin_plot.multi_panel.multi_panel, 
    #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
    figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
    #end if
    scale='$method.violin_plot.scale',
    #if $method.xlabel

                <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
                    <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
                    <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
                        <expand macro="seaborn_color_palette_options"/>
                    </param>
                    <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>            
                </section>
            </when>
            <when value="pl.pca">
                <expand macro="param_color"/>
                <expand macro="param_use_raw"/>

            </when>
            <when value="pl.paga_compare">
                <expand macro="inputs_paga"/>
            </when>
            <when value="pl.paga_path">
                <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" 
                    help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>
                <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
                <expand macro="param_use_raw"/>
                <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
                <expand macro="param_color_map"/>

                <expand macro="pl_rank_genes_groups_ext"/>
                <expand macro="params_plots"/>
                <expand macro="pl_stacked_violin"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
            <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
        </data>

        </data>
        <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
            <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
            <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <!-- test 1: pl.scatter !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.scatter"/>
                <conditional name="type">

                    <param name="palette" value="inferno"/>
                    <param name="frameon" value="True"/>
                    <param name="size" value="1"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.scatter"/>
                <has_text_matching expression="basis='umap'" />
                <has_text_matching expression="color=\['HES4'\]"/>
                <has_text_matching expression="use_raw=True"/>
                <has_text_matching expression="sort_order=True"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontsize=1"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="color_map='inferno'"/>
                <has_text_matching expression="palette='inferno'"/>
                <has_text_matching expression="frameon=True"/>
                <has_text_matching expression="size=1.0"/>
            </assert_stdout>
            <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 2: pl.scatter !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.scatter"/>
                <conditional name="type">

                    <param name="frameon" value="False"/>
                    <param name="size" value="1"/>
                    <param name="title" value="A title"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.scatter"/>
                <has_text_matching expression="x='EKLF'" />
                <has_text_matching expression="y='Cebpa'"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="sort_order=True"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontsize=1"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="palette='bwr'"/>
                <has_text_matching expression="frameon=False"/>
                <has_text_matching expression="size=1.0"/>
                <has_text_matching expression="title='A title'"/>
            </assert_stdout>
            <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 3: pl.heatmap !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.heatmap"/>
                <conditional name="var_names">

                    <param name="cmap" value="YlGnBu"/>
                    <param name="interpolation" value="None"/>
                    <param name="origin" value="upper"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.heatmap"/>
                <has_text_matching expression="var_names=adata.var_names" />
                <has_text_matching expression="groupby='cell_type'"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="num_categories=7"/>
                <has_text_matching expression="dendrogram=True"/>
                <has_text_matching expression="figsize=\(10, 3\)"/>
                <has_text_matching expression="swap_axes=True"/>
                <has_text_matching expression="show_gene_labels=False"/>
                <has_text_matching expression="cmap='YlGnBu'"/>
                <has_text_matching expression="origin='upper'"/>
            </assert_stdout>
            <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 4: pl.dotplot !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dotplot"/>
                <conditional name="var_names">

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0" />
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.dotplot"/>
                <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />
                <has_text_matching expression="groupby='louvain'"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="num_categories=7"/>
                <has_text_matching expression="dendrogram=True"/>
                <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
                <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
                <has_text_matching expression="color_map='hot'"/>
                <has_text_matching expression="dot_max=0.7"/>
                <has_text_matching expression="dot_min=0.1"/>
                <has_text_matching expression="linewidths=0.0"/>
                <has_text_matching expression="edgecolors='face'"/>
            </assert_stdout>
            <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 5: pl.violin !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.violin"/>
                <conditional name="key_variables">

                    <param name="color" value="AliceBlue"/>
                    <param name="palette" value="viridis"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.violin"/>
                <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="stripplot=True"/>
                <has_text_matching expression="jitter=True"/>
                <has_text_matching expression="size=1"/>
                <has_text_matching expression="multi_panel=True"/>
                <has_text_matching expression="figsize=\(20, 20\)"/>
                <has_text_matching expression="scale='width'"/>
                <has_text_matching expression="bw='scott'"/>
                <has_text_matching expression="scale='width'"/>
                <has_text_matching expression="linewidth=0.0"/>
                <has_text_matching expression="color='AliceBlue'"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="saturation=0.75"/>
            </assert_stdout>
            <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 6: pl.stacked_violin !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.stacked_violin"/>
                <conditional name="var_names">

                    <param name="color" value="AliceBlue"/>
                    <param name="palette" value="viridis"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.stacked_violin"/>
                <has_text_matching expression="groupby='cell_type'"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="num_categories=7"/>
                <has_text_matching expression="dendrogram=True"/>
                <has_text_matching expression="swap_axes=True"/>
                <has_text_matching expression="stripplot=True"/>
                <has_text_matching expression="jitter=True"/>
                <has_text_matching expression="size=1"/>
                <has_text_matching expression="scale='width'"/>
                <has_text_matching expression="bw='scott'"/>
                <has_text_matching expression="scale='width'"/>
                <has_text_matching expression="linewidth=0.0"/>
                <has_text_matching expression="color='AliceBlue'"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="saturation=0.75"/>
            </assert_stdout>
            <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 7: pl.matrixplot !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.matrixplot"/>
                <conditional name="var_names">

                    <param name="cmap" value="viridis"/>
                    <param name="edgecolors" value="face"/>
                    <param name="snap" value="False"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.matrixplot"/>
                <has_text_matching expression="var_names=adata.var_names" />
                <has_text_matching expression="groupby='cell_type'"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="num_categories=7"/>
                <has_text_matching expression="dendrogram=True"/>
                <has_text_matching expression="swap_axes=True"/>
                <has_text_matching expression="cmap='viridis'"/>
                <has_text_matching expression="edgecolors='face'"/>
                <has_text_matching expression="snap=False"/>
            </assert_stdout>
            <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 8: pl.clustermap !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.clustermap"/>
                <param name="use_raw" value="False"/>

                    <param name="standard_scale" value="None"/>
                    <param name="col_cluster" value="False"/>
                    <param name="row_cluster" value="False"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.clustermap"/>
                <has_text_matching expression="adata=adata" />
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="method='single'"/>
                <has_text_matching expression="metric='euclidean'"/>
                <has_text_matching expression="col_cluster=False"/>
                <has_text_matching expression="row_cluster=False"/>
            </assert_stdout>
            <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 9: pl.highest_expr_genes !-->
            <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.highest_expr_genes"/>
                <param name="n_top" value="30"/>

                <section name="setseaborn_boxplot">
                    <param name="color" value="blue"/>
                    <param name="saturation" value="0.5"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.highest_expr_genes"/>
                <has_text_matching expression="n_top=30" />
                <has_text_matching expression="gene_symbols='means'" />
                <has_text_matching expression="color='blue'"/>
                <has_text_matching expression="saturation=0.5"/>
            </assert_stdout>
            <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 10: pl.highly_variable_genes !-->
            <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.highly_variable_genes"/>
                <param name="log" value="false"/>
                <param name="highly_variable_genes" value="true"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.highly_variable_genes"/>
                <has_text_matching expression="adata_or_result=adata" />
                <has_text_matching expression="log=False" />
                <has_text_matching expression="highly_variable_genes=True"/>
            </assert_stdout>
            <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 11: pl.pca !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="pl.pca"/>
                <param name="color" value="CD3D,CD79A"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.pca"/>
                <has_text_matching expression="save='.pdf'" />
                <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />
                <has_text_matching expression="use_raw=False" />
                <has_text_matching expression="sort_order=True" />
                <has_text_matching expression="components=\['1,2', '1,3'\]" />
                <has_text_matching expression="projection='2d'" />
                <has_text_matching expression="legend_loc='right margin'" />
                <has_text_matching expression="legend_fontsize=1" />
                <has_text_matching expression="legend_fontweight='normal'" />
                <has_text_matching expression="size=1.0" />
                <has_text_matching expression="palette='viridis'" />
                <has_text_matching expression="frameon=True" />
                <has_text_matching expression="ncols=2" />
                <has_text_matching expression="wspace=0.1" />
                <has_text_matching expression="hspace=0.25" />
                <has_text_matching expression="linewidths=0.0" />
                <has_text_matching expression="edgecolors='face" />
            </assert_stdout>
            <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <!-- test 12: pl.pca_loadings !-->
            <param name="adata" value="pp.pca.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.pca_loadings"/>
                <param name="components" value="1,2,3"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.pca_loadings"/>
                <has_text_matching expression="components=\[1, 2, 3\]" />
            </assert_stdout>
            <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 13: pl.pca_variance_ratio !-->
            <param name="adata" value="pp.pca.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.pca_variance_ratio"/>
                <param name="n_pcs" value="5"/>
                <param name="log" value="False"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.pca_variance_ratio"/>
                <has_text_matching expression="n_pcs=5" />
                <has_text_matching expression="log=False" />
            </assert_stdout>
            <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 14: pl.pca_overview !-->
            <param name="adata" value="pp.pca.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.pca_overview"/>
                <param name="use_raw" value="False"/>

                    <param name="ncols" value="4"/>
                    <param name="wspace" value="0.1"/>
                    <param name="hspace" value="0.25"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.pca_overview"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="sort_order=True"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontsize=1"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="size=1.0"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="frameon=True"/>
                <has_text_matching expression="ncols=4"/>
                <has_text_matching expression="wspace=0.1"/>
                <has_text_matching expression="hspace=0.25"/>
            </assert_stdout>
            <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 15: pl.tsne !-->
            <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.tsne"/>
                <param name="use_raw" value="False"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.tsne"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="edges=False"/>
                <has_text_matching expression="arrows=False"/>
                <has_text_matching expression="sort_order=True"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontsize=1"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="size=1.0"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="frameon=True"/>
                <has_text_matching expression="ncols=4"/>
                <has_text_matching expression="wspace=0.1"/>
                <has_text_matching expression="hspace=0.25"/>
                <has_text_matching expression="linewidths=0.0"/>
                <has_text_matching expression="edgecolors='face'"/>
            </assert_stdout>
            <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 16: pl.umap !-->
            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.umap"/>
                <param name="color" value="paul15_clusters"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.umap"/>
                <has_text_matching expression="color=\['paul15_clusters'\]"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="edges=True"/>
                <has_text_matching expression="edges_width=0.1"/>
                <has_text_matching expression="edges_color='AliceBlue'"/>
                <has_text_matching expression="arrows=False"/>
                <has_text_matching expression="sort_order=True"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontsize=1"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="size=1.0"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="frameon=True"/>
                <has_text_matching expression="ncols=4"/>
                <has_text_matching expression="wspace=0.1"/>
                <has_text_matching expression="hspace=0.25"/>
                <has_text_matching expression="linewidths=0.0"/>
                <has_text_matching expression="edgecolors='face'"/>
            </assert_stdout>
            <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 17: pl.diffmap !-->
            <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.diffmap"/>
                <param name="color" value="paul15_clusters"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.diffmap"/>
                <has_text_matching expression="color=\['paul15_clusters'\]"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="sort_order=True"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontsize=1"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="size=1.0"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="frameon=True"/>
                <has_text_matching expression="ncols=4"/>
                <has_text_matching expression="wspace=0.1"/>
                <has_text_matching expression="hspace=0.25"/>
                <has_text_matching expression="linewidths=0.0"/>
                <has_text_matching expression="edgecolors='face'"/>
            </assert_stdout>
            <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 18: pl.draw_graph !-->
            <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.draw_graph"/>
                <param name="use_raw" value="false"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.draw_graph"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="edges=True"/>
                <has_text_matching expression="edges_width=0.1"/>
                <has_text_matching expression="edges_color='Crimson'"/>
                <has_text_matching expression="arrows=False"/>
                <has_text_matching expression="sort_order=False"/>
                <has_text_matching expression="projection='2d'"/>
                <has_text_matching expression="legend_loc='right margin'"/>
                <has_text_matching expression="legend_fontweight='normal'"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="frameon=True"/>
                <has_text_matching expression="ncols=4"/>
                <has_text_matching expression="wspace=0.1"/>
                <has_text_matching expression="hspace=0.25"/>
                <has_text_matching expression="linewidths=0.0"/>
                <has_text_matching expression="edgecolors='face"/>
            </assert_stdout>
            <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
        </test>
        <!--<test>
            < test pl.dpt_groups_pseudotime >
            <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

                <has_text_matching expression="color_map='viridis'"/>
            </assert_stdout>
            <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>!-->
        <test>
            <!-- test 19: pl.dpt_timeseries !-->
            <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dpt_timeseries"/>
                <conditional name="heatmap">
                    <param name="as_heatmap" value="True"/>
                    <param name="color_map" value="viridis"/>
                </conditional>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.dpt_timeseries"/>
                <has_text_matching expression="color_map='viridis'"/>
                <has_text_matching expression="as_heatmap=True"/>
            </assert_stdout>
            <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>
        <!--<test>
             test pl.paga
            <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />

        <!--<test>
             test pl.paga_compare
        </test>!-->
        <!--<test>
             test pl.paga_path
        </test>!-->  
        <test>
            <!-- test 20: pl.rank_genes_groups !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups"/>
                <param name="n_genes" value="10"/>
                <param name="fontsize" value="8"/>
                <param name="ncols" value="4"/>
                <param name="sharey" value="true"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.rank_genes_groups"/>
                <has_text_matching expression="n_genes=10"/>
                <has_text_matching expression="fontsize=8"/>
                <has_text_matching expression="ncols=4"/>
                <has_text_matching expression="sharey=True"/>
            </assert_stdout>
            <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 21: pl.rank_genes_groups_violin !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_violin"/>
                <conditional name="genes">

                        <param name="size" value="1"/>
                    </conditional>
                    <param name="scale" value="width"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
                <has_text_matching expression="n_genes=10"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="split=True"/>
                <has_text_matching expression="strip=True"/>
                <has_text_matching expression="jitter=True"/>
                <has_text_matching expression="size=1"/>
                <has_text_matching expression="scale='width'"/>
            </assert_stdout>
            <output_collection name="collection_png">
                <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
            </output_collection>
        </test>
        <test>
            <!-- test 22: pl.rank_genes_groups_dotplot !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_dotplot"/>
                <param name="n_genes" value="10"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0" />
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
                <has_text_matching expression="n_genes=10"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="dendrogram=False"/>
                <has_text_matching expression="color_map='viridis'"/>
                <has_text_matching expression="linewidths=0.0"/>
                <has_text_matching expression="edgecolors='face'"/>
            </assert_stdout>
            <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 23: pl.rank_genes_groups_heatmap !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_heatmap"/>
                <param name="n_genes" value="10"/>

                    <param name="cmap" value="viridis"/>
                    <param name="interpolation" value="None"/>
                    <param name="origin" value="upper"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/>
                <has_text_matching expression="n_genes=10"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="dendrogram=False"/>
                <has_text_matching expression="swap_axes=False"/>
                <has_text_matching expression="show_gene_labels=False"/>
                <has_text_matching expression="cmap='viridis'"/>
                <has_text_matching expression="origin='upper'"/>
            </assert_stdout>
            <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 24: pl.rank_genes_groups_matrixplot !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_matrixplot"/>
                <param name="n_genes" value="10"/>

                    <param name="cmap" value="viridis"/>
                    <param name="edgecolors" value="face"/>
                    <param name="snap" value="False"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/>
                <has_text_matching expression="n_genes=10"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="dendrogram=False"/>
                <has_text_matching expression="swap_axes=False"/>
                <has_text_matching expression="cmap='viridis'"/>
                <has_text_matching expression="edgecolors='face'"/>
                <has_text_matching expression="snap=False"/>
            </assert_stdout>
            <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 25: pl.rank_genes_groups_stacked_violin !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
                <param name="n_genes" value="10"/>

                    <param name="color" value="AliceBlue"/>
                    <param name="palette" value="viridis"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
                <has_text_matching expression="n_genes=10"/>
                <has_text_matching expression="log=False"/>
                <has_text_matching expression="use_raw=False"/>
                <has_text_matching expression="dendrogram=True"/>
                <has_text_matching expression="swap_axes=True"/>
                <has_text_matching expression="stripplot=True"/>
                <has_text_matching expression="jitter=True"/>
                <has_text_matching expression="size=1"/>
                <has_text_matching expression="scale='width'"/>
                <has_text_matching expression="bw='scott'"/>
                <has_text_matching expression="scale='width'"/>
                <has_text_matching expression="linewidth=0.0"/>
                <has_text_matching expression="color='AliceBlue'"/>
                <has_text_matching expression="palette='viridis'"/>
                <has_text_matching expression="saturation=0.75"/>
            </assert_stdout>
            <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Generic: Scatter plot along observations or variables axes (`pl.scatter`)

<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__

Generic: Stacked violin plots (`pl.stacked_violin`)
===================================================

Makes a compact image composed of individual violin plots (from `seaborn.violinplot`) 
stacked on top of each other. Useful to visualize gene expression per cluster.

More details on the `scanpy documentation
<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__

6:dbbe1ea8ecb1

    groupby='$method.groupby',
    #end if
    log=$method.log,
    use_raw=$method.use_raw,
    @CMD_conditional_stripplot@
    multi_panel=$method.violin_plot.multi_panel.multi_panel,
    #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
    figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
    #end if
    scale='$method.violin_plot.scale',
    #if $method.xlabel

                <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
                    <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
                    <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
                        <expand macro="seaborn_color_palette_options"/>
                    </param>
                    <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>
                </section>
            </when>
            <when value="pl.pca">
                <expand macro="param_color"/>
                <expand macro="param_use_raw"/>

            </when>
            <when value="pl.paga_compare">
                <expand macro="inputs_paga"/>
            </when>
            <when value="pl.paga_path">
                <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
                    help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>
                <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
                <expand macro="param_use_raw"/>
                <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
                <expand macro="param_color_map"/>

                <expand macro="pl_rank_genes_groups_ext"/>
                <expand macro="params_plots"/>
                <expand macro="pl_stacked_violin"/>
            </when>
        </conditional>
        <expand macro="inputs_common_advanced"/>
    </inputs>
    <outputs>
        <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
            <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
        </data>

        </data>
        <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
            <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
            <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
        </collection>
        <data name="hidden_output" format="txt" label="Log file" hidden="true" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <!-- test 0: pl.scatter !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.scatter"/>
                <conditional name="type">

                    <param name="palette" value="inferno"/>
                    <param name="frameon" value="True"/>
                    <param name="size" value="1"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.scatter"/>
                    <has_text_matching expression="basis='umap'" />
                    <has_text_matching expression="color=\['HES4'\]"/>
                    <has_text_matching expression="use_raw=True"/>
                    <has_text_matching expression="sort_order=True"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontsize=1"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="color_map='inferno'"/>
                    <has_text_matching expression="palette='inferno'"/>
                    <has_text_matching expression="frameon=True"/>
                    <has_text_matching expression="size=1.0"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 1: pl.scatter !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.scatter"/>
                <conditional name="type">

                    <param name="frameon" value="False"/>
                    <param name="size" value="1"/>
                    <param name="title" value="A title"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.scatter"/>
                    <has_text_matching expression="x='EKLF'" />
                    <has_text_matching expression="y='Cebpa'"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="sort_order=True"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontsize=1"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="palette='bwr'"/>
                    <has_text_matching expression="frameon=False"/>
                    <has_text_matching expression="size=1.0"/>
                    <has_text_matching expression="title='A title'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 2: pl.heatmap !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.heatmap"/>
                <conditional name="var_names">

                    <param name="cmap" value="YlGnBu"/>
                    <param name="interpolation" value="None"/>
                    <param name="origin" value="upper"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.heatmap"/>
                    <has_text_matching expression="var_names=adata.var_names" />
                    <has_text_matching expression="groupby='cell_type'"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="num_categories=7"/>
                    <has_text_matching expression="dendrogram=True"/>
                    <has_text_matching expression="figsize=\(10, 3\)"/>
                    <has_text_matching expression="swap_axes=True"/>
                    <has_text_matching expression="show_gene_labels=False"/>
                    <has_text_matching expression="cmap='YlGnBu'"/>
                    <has_text_matching expression="origin='upper'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 3: pl.dotplot !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dotplot"/>
                <conditional name="var_names">

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0" />
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.dotplot"/>
                    <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />
                    <has_text_matching expression="groupby='louvain'"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="num_categories=7"/>
                    <has_text_matching expression="dendrogram=True"/>
                    <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
                    <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
                    <has_text_matching expression="color_map='hot'"/>
                    <has_text_matching expression="dot_max=0.7"/>
                    <has_text_matching expression="dot_min=0.1"/>
                    <has_text_matching expression="linewidths=0.0"/>
                    <has_text_matching expression="edgecolors='face'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 4: pl.violin !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.violin"/>
                <conditional name="key_variables">

                    <param name="color" value="AliceBlue"/>
                    <param name="palette" value="viridis"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.violin"/>
                    <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="stripplot=True"/>
                    <has_text_matching expression="jitter=True"/>
                    <has_text_matching expression="size=1"/>
                    <has_text_matching expression="multi_panel=True"/>
                    <has_text_matching expression="figsize=\(20, 20\)"/>
                    <has_text_matching expression="scale='width'"/>
                    <has_text_matching expression="bw='scott'"/>
                    <has_text_matching expression="scale='width'"/>
                    <has_text_matching expression="linewidth=0.0"/>
                    <has_text_matching expression="color='AliceBlue'"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="saturation=0.75"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 5: pl.stacked_violin !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.stacked_violin"/>
                <conditional name="var_names">

                    <param name="color" value="AliceBlue"/>
                    <param name="palette" value="viridis"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.stacked_violin"/>
                    <has_text_matching expression="groupby='cell_type'"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="num_categories=7"/>
                    <has_text_matching expression="dendrogram=True"/>
                    <has_text_matching expression="swap_axes=True"/>
                    <has_text_matching expression="stripplot=True"/>
                    <has_text_matching expression="jitter=True"/>
                    <has_text_matching expression="size=1"/>
                    <has_text_matching expression="scale='width'"/>
                    <has_text_matching expression="bw='scott'"/>
                    <has_text_matching expression="scale='width'"/>
                    <has_text_matching expression="linewidth=0.0"/>
                    <has_text_matching expression="color='AliceBlue'"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="saturation=0.75"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 6: pl.matrixplot !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.matrixplot"/>
                <conditional name="var_names">

                    <param name="cmap" value="viridis"/>
                    <param name="edgecolors" value="face"/>
                    <param name="snap" value="False"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.matrixplot"/>
                    <has_text_matching expression="var_names=adata.var_names" />
                    <has_text_matching expression="groupby='cell_type'"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="num_categories=7"/>
                    <has_text_matching expression="dendrogram=True"/>
                    <has_text_matching expression="swap_axes=True"/>
                    <has_text_matching expression="cmap='viridis'"/>
                    <has_text_matching expression="edgecolors='face'"/>
                    <has_text_matching expression="snap=False"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 7: pl.clustermap !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.clustermap"/>
                <param name="use_raw" value="False"/>

                    <param name="standard_scale" value="None"/>
                    <param name="col_cluster" value="False"/>
                    <param name="row_cluster" value="False"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.clustermap"/>
                    <has_text_matching expression="adata=adata" />
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="method='single'"/>
                    <has_text_matching expression="metric='euclidean'"/>
                    <has_text_matching expression="col_cluster=False"/>
                    <has_text_matching expression="row_cluster=False"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 8: pl.highest_expr_genes !-->
            <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.highest_expr_genes"/>
                <param name="n_top" value="30"/>

                <section name="setseaborn_boxplot">
                    <param name="color" value="blue"/>
                    <param name="saturation" value="0.5"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.highest_expr_genes"/>
                    <has_text_matching expression="n_top=30" />
                    <has_text_matching expression="gene_symbols='means'" />
                    <has_text_matching expression="color='blue'"/>
                    <has_text_matching expression="saturation=0.5"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 9: pl.highly_variable_genes !-->
            <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.highly_variable_genes"/>
                <param name="log" value="false"/>
                <param name="highly_variable_genes" value="true"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.highly_variable_genes"/>
                    <has_text_matching expression="adata_or_result=adata" />
                    <has_text_matching expression="log=False" />
                    <has_text_matching expression="highly_variable_genes=True"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 10: pl.pca !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="pl.pca"/>
                <param name="color" value="CD3D,CD79A"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.pca"/>
                    <has_text_matching expression="save='.pdf'" />
                    <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />
                    <has_text_matching expression="use_raw=False" />
                    <has_text_matching expression="sort_order=True" />
                    <has_text_matching expression="components=\['1,2', '1,3'\]" />
                    <has_text_matching expression="projection='2d'" />
                    <has_text_matching expression="legend_loc='right margin'" />
                    <has_text_matching expression="legend_fontsize=1" />
                    <has_text_matching expression="legend_fontweight='normal'" />
                    <has_text_matching expression="size=1.0" />
                    <has_text_matching expression="palette='viridis'" />
                    <has_text_matching expression="frameon=True" />
                    <has_text_matching expression="ncols=2" />
                    <has_text_matching expression="wspace=0.1" />
                    <has_text_matching expression="hspace=0.25" />
                    <has_text_matching expression="linewidths=0.0" />
                    <has_text_matching expression="edgecolors='face" />
                </assert_contents>
            </output>
            <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <!-- test 11: pl.pca_loadings !-->
            <param name="adata" value="pp.pca.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.pca_loadings"/>
                <param name="components" value="1,2,3"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.pca_loadings"/>
                    <has_text_matching expression="components=\[1, 2, 3\]" />
                </assert_contents>
            </output>
            <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 12: pl.pca_variance_ratio !-->
            <param name="adata" value="pp.pca.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.pca_variance_ratio"/>
                <param name="n_pcs" value="5"/>
                <param name="log" value="False"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.pca_variance_ratio"/>
                    <has_text_matching expression="n_pcs=5" />
                    <has_text_matching expression="log=False" />
                </assert_contents>
            </output>
            <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 13: pl.pca_overview !-->
            <param name="adata" value="pp.pca.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.pca_overview"/>
                <param name="use_raw" value="False"/>

                    <param name="ncols" value="4"/>
                    <param name="wspace" value="0.1"/>
                    <param name="hspace" value="0.25"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.pca_overview"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="sort_order=True"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontsize=1"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="size=1.0"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="frameon=True"/>
                    <has_text_matching expression="ncols=4"/>
                    <has_text_matching expression="wspace=0.1"/>
                    <has_text_matching expression="hspace=0.25"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 14: pl.tsne !-->
            <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.tsne"/>
                <param name="use_raw" value="False"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.tsne"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="edges=False"/>
                    <has_text_matching expression="arrows=False"/>
                    <has_text_matching expression="sort_order=True"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontsize=1"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="size=1.0"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="frameon=True"/>
                    <has_text_matching expression="ncols=4"/>
                    <has_text_matching expression="wspace=0.1"/>
                    <has_text_matching expression="hspace=0.25"/>
                    <has_text_matching expression="linewidths=0.0"/>
                    <has_text_matching expression="edgecolors='face'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 15: pl.umap !-->
            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.umap"/>
                <param name="color" value="paul15_clusters"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.umap"/>
                    <has_text_matching expression="color=\['paul15_clusters'\]"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="edges=True"/>
                    <has_text_matching expression="edges_width=0.1"/>
                    <has_text_matching expression="edges_color='AliceBlue'"/>
                    <has_text_matching expression="arrows=False"/>
                    <has_text_matching expression="sort_order=True"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontsize=1"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="size=1.0"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="frameon=True"/>
                    <has_text_matching expression="ncols=4"/>
                    <has_text_matching expression="wspace=0.1"/>
                    <has_text_matching expression="hspace=0.25"/>
                    <has_text_matching expression="linewidths=0.0"/>
                    <has_text_matching expression="edgecolors='face'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 16: pl.diffmap !-->
            <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.diffmap"/>
                <param name="color" value="paul15_clusters"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.diffmap"/>
                    <has_text_matching expression="color=\['paul15_clusters'\]"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="sort_order=True"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontsize=1"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="size=1.0"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="frameon=True"/>
                    <has_text_matching expression="ncols=4"/>
                    <has_text_matching expression="wspace=0.1"/>
                    <has_text_matching expression="hspace=0.25"/>
                    <has_text_matching expression="linewidths=0.0"/>
                    <has_text_matching expression="edgecolors='face'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 17: pl.draw_graph !-->
            <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.draw_graph"/>
                <param name="use_raw" value="false"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0"/>
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.draw_graph"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="edges=True"/>
                    <has_text_matching expression="edges_width=0.1"/>
                    <has_text_matching expression="edges_color='Crimson'"/>
                    <has_text_matching expression="arrows=False"/>
                    <has_text_matching expression="sort_order=False"/>
                    <has_text_matching expression="projection='2d'"/>
                    <has_text_matching expression="legend_loc='right margin'"/>
                    <has_text_matching expression="legend_fontweight='normal'"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="frameon=True"/>
                    <has_text_matching expression="ncols=4"/>
                    <has_text_matching expression="wspace=0.1"/>
                    <has_text_matching expression="hspace=0.25"/>
                    <has_text_matching expression="linewidths=0.0"/>
                    <has_text_matching expression="edgecolors='face"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
        </test>
        <!--<test>
            < test pl.dpt_groups_pseudotime >
            <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

                <has_text_matching expression="color_map='viridis'"/>
            </assert_stdout>
            <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>!-->
        <test>
            <!-- test 18: pl.dpt_timeseries !-->
            <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dpt_timeseries"/>
                <conditional name="heatmap">
                    <param name="as_heatmap" value="True"/>
                    <param name="color_map" value="viridis"/>
                </conditional>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.dpt_timeseries"/>
                    <has_text_matching expression="color_map='viridis'"/>
                    <has_text_matching expression="as_heatmap=True"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
        </test>
        <!--<test>
             test pl.paga
            <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />

        <!--<test>
             test pl.paga_compare
        </test>!-->
        <!--<test>
             test pl.paga_path
        </test>!-->
        <test>
            <!-- test 19: pl.rank_genes_groups !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups"/>
                <param name="n_genes" value="10"/>
                <param name="fontsize" value="8"/>
                <param name="ncols" value="4"/>
                <param name="sharey" value="true"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.rank_genes_groups"/>
                    <has_text_matching expression="n_genes=10"/>
                    <has_text_matching expression="fontsize=8"/>
                    <has_text_matching expression="ncols=4"/>
                    <has_text_matching expression="sharey=True"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 20: pl.rank_genes_groups_violin !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_violin"/>
                <conditional name="genes">

                        <param name="size" value="1"/>
                    </conditional>
                    <param name="scale" value="width"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
                    <has_text_matching expression="n_genes=10"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="split=True"/>
                    <has_text_matching expression="strip=True"/>
                    <has_text_matching expression="jitter=True"/>
                    <has_text_matching expression="size=1"/>
                    <has_text_matching expression="scale='width'"/>
                </assert_contents>
            </output>
            <output_collection name="collection_png">
                <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
                <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
            </output_collection>
        </test>
        <test>
            <!-- test 21: pl.rank_genes_groups_dotplot !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_dotplot"/>
                <param name="n_genes" value="10"/>

                <section name="matplotlib_pyplot_scatter">
                    <param name="linewidths" value="0" />
                    <param name="edgecolors" value="face"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
                    <has_text_matching expression="n_genes=10"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="dendrogram=False"/>
                    <has_text_matching expression="color_map='viridis'"/>
                    <has_text_matching expression="linewidths=0.0"/>
                    <has_text_matching expression="edgecolors='face'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 22: pl.rank_genes_groups_heatmap !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_heatmap"/>
                <param name="n_genes" value="10"/>

                    <param name="cmap" value="viridis"/>
                    <param name="interpolation" value="None"/>
                    <param name="origin" value="upper"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/>
                    <has_text_matching expression="n_genes=10"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="dendrogram=False"/>
                    <has_text_matching expression="swap_axes=False"/>
                    <has_text_matching expression="show_gene_labels=False"/>
                    <has_text_matching expression="cmap='viridis'"/>
                    <has_text_matching expression="origin='upper'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 23: pl.rank_genes_groups_matrixplot !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_matrixplot"/>
                <param name="n_genes" value="10"/>

                    <param name="cmap" value="viridis"/>
                    <param name="edgecolors" value="face"/>
                    <param name="snap" value="False"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/>
                    <has_text_matching expression="n_genes=10"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="dendrogram=False"/>
                    <has_text_matching expression="swap_axes=False"/>
                    <has_text_matching expression="cmap='viridis'"/>
                    <has_text_matching expression="edgecolors='face'"/>
                    <has_text_matching expression="snap=False"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 24: pl.rank_genes_groups_stacked_violin !-->
            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
                <param name="n_genes" value="10"/>

                    <param name="color" value="AliceBlue"/>
                    <param name="palette" value="viridis"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
                    <has_text_matching expression="n_genes=10"/>
                    <has_text_matching expression="log=False"/>
                    <has_text_matching expression="use_raw=False"/>
                    <has_text_matching expression="dendrogram=True"/>
                    <has_text_matching expression="swap_axes=True"/>
                    <has_text_matching expression="stripplot=True"/>
                    <has_text_matching expression="jitter=True"/>
                    <has_text_matching expression="size=1"/>
                    <has_text_matching expression="scale='width'"/>
                    <has_text_matching expression="bw='scott'"/>
                    <has_text_matching expression="scale='width'"/>
                    <has_text_matching expression="linewidth=0.0"/>
                    <has_text_matching expression="color='AliceBlue'"/>
                    <has_text_matching expression="palette='viridis'"/>
                    <has_text_matching expression="saturation=0.75"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Generic: Scatter plot along observations or variables axes (`pl.scatter`)

<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__

Generic: Stacked violin plots (`pl.stacked_violin`)
===================================================

Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
stacked on top of each other. Useful to visualize gene expression per cluster.

More details on the `scanpy documentation
<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__