comparison plot.xml @ 8:6adf98e782f3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"

7:7647e5cd1b8b

    @CMD_params_groups@
    @CMD_params_pl_components@
    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    #if $method.plot.palette != 'default'
    palette='$method.plot.palette',
    #end if
    #if $method.plot.color_map != 'None'
    color_map='$method.plot.color_map',
    #end if
    @CMD_param_legend_fontsize@

    @CMD_param_color@
    #if str($method.gene_symbols) != ''
    gene_symbols='$method.gene_symbols',
    #end if
    use_raw=$method.use_raw,
    #if str($method.layout) != 'None'
    layout='$method.layout',
    #end if
    edges=$method.edges.edges,
    #if str($method.edges.edges) == 'True'
    edges_width=$method.edges.edges_width,
    edges_color='$method.edges.edges_color',
    #end if

                <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
                <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
                <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
                <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
                <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
                <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
                <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
                <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
                <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
                <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
            </param>

            </when>
            <when value="pl.draw_graph">
                <expand macro="param_color"/>
                <expand macro="gene_symbols"/>
                <expand macro="param_use_raw"/>
                <param argument="layout" type="select" optional="true" label="Plotting layout" help="">
                    <expand macro="options_layout"/>
                </param>
                <expand macro="pl_edges"/>
                <expand macro="param_arrows"/>
                <expand macro="param_sort_order"/>

                    <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"/>

                    <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>

                    <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>

                <param name="standard_scale" value="None"/>
                <section name="seaborn_violinplot">
                    <param name="bw" value="scott"/>
                    <param name="linewidth" value="0"/>
                    <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" />

                    <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>

            <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"/>
                <conditional name="edges">
                    <param name="edges" value="True"/>
                    <param name="edges_width" value="0.1"/>
                    <param name="edges_color" value="Crimson"/>
                </conditional>

                    <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">

                <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">

                    <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>

8:6adf98e782f3

    @CMD_params_groups@
    @CMD_params_pl_components@
    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    #if $method.plot.palette != 'default'
    palette=['$method.plot.palette'],
    #end if
    #if $method.plot.color_map != 'None'
    color_map='$method.plot.color_map',
    #end if
    @CMD_param_legend_fontsize@

    @CMD_param_color@
    #if str($method.gene_symbols) != ''
    gene_symbols='$method.gene_symbols',
    #end if
    use_raw=$method.use_raw,
    layout='$method.layout',
    edges=$method.edges.edges,
    #if str($method.edges.edges) == 'True'
    edges_width=$method.edges.edges_width,
    edges_color='$method.edges.edges_color',
    #end if

                <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
                <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
                <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
                <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
                <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
                <!-- doesn't currenty work: https://github.com/galaxyproject/tools-iuc/pull/3485#issuecomment-800055967
                <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
                -->
                <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
                <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
                <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
                <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
            </param>

            </when>
            <when value="pl.draw_graph">
                <expand macro="param_color"/>
                <expand macro="gene_symbols"/>
                <expand macro="param_use_raw"/>
                <param argument="layout" type="select" optional="false" label="Plotting layout" help="">
                    <expand macro="options_layout"/>
                </param>
                <expand macro="pl_edges"/>
                <expand macro="param_arrows"/>
                <expand macro="param_sort_order"/>

                    <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="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"/>

                    <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="frameon=False"/>
                    <has_text_matching expression="size=1.0"/>
                    <has_text_matching expression="title='A title'"/>
                </assert_contents>
            </output>

                    <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="saturation=0.75"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
        </test>

                <param name="standard_scale" value="None"/>
                <section name="seaborn_violinplot">
                    <param name="bw" value="scott"/>
                    <param name="linewidth" value="0"/>
                    <param name="color" value="AliceBlue"/>
                    <param name="saturation" value="0.75"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />

                    <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="saturation=0.75"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>

            <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"/>
                <param name="layout" value="fr"/>
                <conditional name="edges">
                    <param name="edges" value="True"/>
                    <param name="edges_width" value="0.1"/>
                    <param name="edges_color" value="Crimson"/>
                </conditional>

                    <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 20: pl.rank_genes_groups_violin, currently broken
        <test>
            <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">

                <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">

                    <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="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>