comparison plot.xml @ 2:c520f64ffd57 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat commit 0c7884b059c6a12ecf22a025317f04c160962be7

1:fee4b4eb0ef5

        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[

    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
    combine = TRUE
)

#else if $method.method == 'DimHeatmap'
plot<-DimHeatmap(
    seurat_obj,
    dims = $method.dims,
    nfeatures = $method.nfeatures,

    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    alpha = $method.plot.alpha,
    order = $method.plot.order,
    min.cutoff = 'q$method.adv.min_cutoff',
    max.cutoff = 'q$method.adv.max_cutoff',
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    by.col = $method.plot.blend.by_col,
    #end if
    keep.scale = '$method.plot.keep_scale',

                <option value="FeatureScatter">Scatter Plot with 'FeatureScatter'</option>
                <option value="CellScatter">Scatter Plot with 'CellScatter'</option>
                <option value="VariableFeaturePlot">Plot Variable Genes with 'VariableFeaturePlot'</option>
                <option value="VizDimLoadings">Visualize Reduction Results with 'VizDimLoadings'</option>
                <option value="DimPlot">Visualize Dimensional Reduction with 'DimPlot'</option>
                <option value="DimHeatmap">Visualize Reduction Results with 'DimHeatmap'</option>
                <option value="ElbowPlot">Determine dimensionality with 'ElbowPlot'</option>
                <option value="FeaturePlot">Visualize expression with 'FeaturePlot'</option>
                <option value="DoHeatmap">Visualize expression with 'DoHeatmap'</option>
                <option value="DotPlot">Visualize expression with 'DotPlot'</option>

                            <param name="sizes_highlight" type="integer" value="1" label="Size of highlighted cells" help="(sizes.highlight)"/>
                        </when>
                        <when value="false">
                        </when>
                    </conditional>
                    <param name="na_value" type="select" label="Colour for NA points when using custom scale" help="(na.value)">
                        <option value="lightgrey" selected="true">lightgrey</option>
                        <option value="grey">grey</option>
                        <option value="black">black</option>
                    </param>
                </section>
                <section name="adv" title="Advanced Options">
                    <param argument="cells" type="data" format="txt,tabular" optional="true" label="List of cells to include on plot" help="text file with one cell on each line"/>
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <param name="shape_by" type="text" optional="true" value="" label="Shape points by a group or identity" help="only when not saving as raster (shape.by)"/>
                </section>
            </when>
            <when value="DimHeatmap">
                <param argument="dims" type="text" value="1:10" label="Dimensions from reduction to plot" help="enter one or a range of dimensions e.g. 3 to plot dim 3, 1:10 to plot dims 1 to 10">
                    <validator type="regex" message="Please only use numbers or colon">^[\d:]+$</validator>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VlnPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/VlnPlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test2: FeatureScatter PDF -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/filtered.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="FeatureScatter"/>
                <param name="feature1" value="nCount_RNA"/>
                <param name="feature2" value="percent.mt"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="FeatureScatter"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/FeatureScatter.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test3: CellScatter PDF -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/variablefeatures.rds"/>
            <param name="plot_format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="CellScatter"/>
                <param name="cell1" value="X16cell"/>
                <param name="cell2" value="midblast.9"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="CellScatter"/>
                </assert_contents>
            </output>
            <output name="plot_out_pdf" location="https://zenodo.org/records/13732784/files/CellScatter.pdf" ftype="pdf" compare="diff" lines_diff="50"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test4: VariableFeaturePlot SVG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/variablefeatures.rds"/>
            <param name="plot_format" value="svg"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VariableFeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_svg" location="https://zenodo.org/records/13732784/files/VariableFeaturePlot.svg" ftype="svg" compare="diff" lines_diff="50"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test5: VizDimLoadings JPEG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="jpeg"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VizDimLoadings"/>
                </assert_contents>
            </output>
            <output name="plot_out_jpeg" location="https://zenodo.org/records/13732784/files/VizDimLoadings.jpeg" ftype="jpeg" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test6: DimPlot TEX -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/umap.rds"/>
            <param name="plot_format" value="tex"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DimPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_tex" location="https://zenodo.org/records/13732784/files/DimPlot.tex" ftype="tex">
                <assert_contents>
                    <has_text_matching expression="beginpicture"/>
                </assert_contents>
            </output>
        </test>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DimHeatmap"/>
                </assert_contents>
            </output>
            <output name="plot_out_tiff" location="https://zenodo.org/records/13732784/files/DimHeatmap.tiff" ftype="tiff" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test8: ElbowPlot EPS -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="eps"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="ElbowPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_eps" location="https://zenodo.org/records/13732784/files/ElbowPlot.eps" ftype="eps"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test9: FeaturePlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/umap.rds"/>
            <param name="plot_format" value="png"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="FeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/FeaturePlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test10: DoHeatmap PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
            <param name="plot_format" value="png"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DoHeatmap"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/DoHeatmap.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test11: DotPlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
            <param name="plot_format" value="png"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DotPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/DotPlot.png" ftype="png" compare="image_diff"/>
        </test>
    </tests>
    <help><![CDATA[
Seurat
======

2:c520f64ffd57

        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <expand macro="creators"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[

    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
    combine = TRUE
)

#else if $method.method == 'ImageDimPlot'

#if $method.adv.cells
    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
    #end if

plot<-ImageDimPlot(
    seurat_obj,
    #if $method.plot.fov != ''
    fov = c(unlist(strsplit(gsub(" ", "", '$method.plot.fov'), ","))),
    #end if
    #if $method.plot.boundaries != ''
    boundaries = c(unlist(strsplit(gsub(" ", "", '$method.plot.boundaries'), ","))),
    #end if
    #if $method.adv.group_by != ''
    group.by = '$method.adv.group_by',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    #end if
    #if $method.plot.cols != ''
    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols'), ","))),
    shuffle.cols = $method.plot.shuffle_cols,
    #end if
    size = $method.plot.size,
    #if $method.plot.molecules != ''
    molecules = c(unlist(strsplit(gsub(" ", "", '$method.plot.molecules'), ","))),
    mols.size = $method.plot.mols_size,
    mols.cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.mols_cols'), ","))),
    mols.alpha = $method.plot.mols_alpha,
    nmols = $method.plot.nmols,
    #end if
    alpha = $method.plot.alpha,
    #if $method.adv.border_color != ''
    border.color = '$method.adv.border_color',
    #end if
    #if $method.adv.border_size != ''
    border.size = $method.adv.border_size,
    #end if
    na.value = '$method.plot.na_value',
    dark.background = $method.adv.dark_background,
    crop = $method.adv.crop,
    #if $method.adv.cells
    cells = c(unlist(strsplit(cells_list, ","))),
    #end if
    overlap = $method.adv.overlap,
    axes = $method.adv.axes,
    combine = TRUE,
    coord.fixed = $method.adv.coord_fixed,
    flip_xy = $method.adv.flip_xy
)

#else if $method.method == 'ImageFeaturePlot'

#if $method.adv.cells
    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
    #end if

plot<-ImageFeaturePlot(
    seurat_obj,
    features = '$method.features',
    #if $method.plot.fov != ''
    fov = c(unlist(strsplit(gsub(" ", "", '$method.plot.fov'), ","))),
    #end if
    #if $method.plot.boundaries != ''
    boundaries = c(unlist(strsplit(gsub(" ", "", '$method.plot.boundaries'), ","))),
    #end if
    size = $method.plot.size,
    #if $method.adv.min_cutoff != ''
    min.cutoff = '$method.adv.min_cutoff',
    #end if
    #if $method.adv.max_cutoff != ''
    max.cutoff = '$method.adv.max_cutoff',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    #end if
    #if $method.plot.molecules != ''
    molecules = c(unlist(strsplit(gsub(" ", "", '$method.plot.molecules'), ","))),
    mols.size = $method.plot.mols_size,
    mols.cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.mols_cols'), ","))),
    nmols = $method.plot.nmols,
    #end if
    alpha = $method.plot.alpha,
    #if $method.adv.border_color != ''
    border.color = '$method.adv.border_color',
    #end if
    #if $method.adv.border_size != ''
    border.size = $method.adv.border_size,
    #end if
    dark.background = $method.adv.dark_background,
    blend = $method.plot.blend,
    #if $method.plot.blend == 'TRUE'
    cols = c("#ff0000", "#00ff00"),
    blend.threshold = $method.plot.blend_threshold,
    #else
    cols = c("lightgrey", "firebrick1"),
    scale = '$method.plot.scale',
    #end if
    crop = $method.adv.crop,
    #if $method.adv.cells
    cells = c(unlist(strsplit(cells_list, ","))),
    #end if
    overlap = $method.adv.overlap,
    axes = $method.adv.axes,
    combine = TRUE,
    coord.fixed = $method.adv.coord_fixed
)

#else if $method.method == 'DimHeatmap'
plot<-DimHeatmap(
    seurat_obj,
    dims = $method.dims,
    nfeatures = $method.nfeatures,

    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    alpha = $method.plot.alpha,
    order = $method.plot.order,
    #if $method.adv.min_cutoff != ''
    min.cutoff = 'q$method.adv.min_cutoff',
    #end if
    #if $method.adv.max_cutoff != ''
    max.cutoff = 'q$method.adv.max_cutoff',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    by.col = $method.plot.blend.by_col,
    #end if
    keep.scale = '$method.plot.keep_scale',

                <option value="FeatureScatter">Scatter Plot with 'FeatureScatter'</option>
                <option value="CellScatter">Scatter Plot with 'CellScatter'</option>
                <option value="VariableFeaturePlot">Plot Variable Genes with 'VariableFeaturePlot'</option>
                <option value="VizDimLoadings">Visualize Reduction Results with 'VizDimLoadings'</option>
                <option value="DimPlot">Visualize Dimensional Reduction with 'DimPlot'</option>
                <option value="ImageDimPlot">Visualize spatial clusters or other categorical groupings with 'ImageDimPlot'</option>
                <option value="ImageFeaturePlot">Visualize expression in a spatial context with 'ImageFeaturePlot'</option>
                <option value="DimHeatmap">Visualize Reduction Results with 'DimHeatmap'</option>
                <option value="ElbowPlot">Determine dimensionality with 'ElbowPlot'</option>
                <option value="FeaturePlot">Visualize expression with 'FeaturePlot'</option>
                <option value="DoHeatmap">Visualize expression with 'DoHeatmap'</option>
                <option value="DotPlot">Visualize expression with 'DotPlot'</option>

                            <param name="sizes_highlight" type="integer" value="1" label="Size of highlighted cells" help="(sizes.highlight)"/>
                        </when>
                        <when value="false">
                        </when>
                    </conditional>
                    <expand macro="plot_na_value"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <expand macro="plot_cells"/>
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <param name="shape_by" type="text" optional="true" value="" label="Shape points by a group or identity" help="only when not saving as raster (shape.by)"/>
                </section>
            </when>
            <when value="ImageDimPlot">
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_fov"/>
                    <expand macro="plot_boundaries"/>
                    <expand macro="plot_cols"/>
                    <expand macro="plot_shuffle_cols"/>
                    <param name="size" type="float" value="1.0" label="Point size for cells" help="(size)"/>
                    <expand macro="plot_alpha"/>
                    <expand macro="plot_molecules"/>
                    <expand macro="plot_mol_alpha"/>
                    <expand macro="plot_nmols"/>
                    <expand macro="plot_na_value"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <expand macro="plot_border"/>
                    <expand macro="plot_dark_background"/>
                    <expand macro="plot_crop"/>
                    <expand macro="plot_cells"/>
                    <expand macro="plot_overlap"/>
                    <expand macro="plot_axes"/>
                    <expand macro="plot_combine"/>
                    <expand macro="plot_coord_fixed"/>
                    <expand macro="plot_flip_xy"/>
                </section>
            </when>
            <when value="ImageFeaturePlot">
                <param argument="features" type="text" value="nFeature_RNA" label="Features to plot" help="comma-separated list e.g. MS4A1, percent.mito, PC_1"/>
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_fov"/>
                    <expand macro="plot_boundaries"/>
                    <param name="size" type="float" value="1.0" label="Point size for cells" help="(size)"/>
                    <expand macro="plot_alpha"/>
                    <expand macro="plot_molecules"/>
                    <expand macro="plot_nmols"/>
                    <param argument="blend" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Scale and blend expression values to visualize coexpression"/>
                    <param name="blend_threshold" type="float" value="0.5" min="0" max="1" label="Colour cutoff from weak signal to strong signal" help="(blend.threshold)"/>
                    <param name="scale" type="select" label="How to handle colour scale across multiple plots" help="(scale)">
                        <option value="feature" selected="true">Scale each feature separately</option>
                        <option value="all">Scale all to same maximum</option>
                        <option value="none">Plots are not scaled</option>
                    </param>
                    <expand macro="raster_select"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <expand macro="plot_border"/>
                    <expand macro="plot_dark_background"/>
                    <expand macro="plot_crop"/>
                    <expand macro="plot_cells"/>
                    <expand macro="plot_coord_fixed"/>
                    <expand macro="plot_overlap"/>
                    <expand macro="plot_axes"/>
                    <expand macro="plot_combine"/>
                    <param name="min_cutoff" type="text" optional="true" value="" label="Minimum cutoff for features - as quantile" help="Minimum values for each feature eg, 'q1'or 'q10')"/>
                    <param name="max_cutoff" type="text" optional="true" value="" label="Maximum cutoff for features - as quantile" help="Maximum values for each feature (eg, 'q1'or 'q10')"/>
                </section>
            </when>
            <when value="DimHeatmap">
                <param argument="dims" type="text" value="1:10" label="Dimensions from reduction to plot" help="enter one or a range of dimensions e.g. 3 to plot dim 3, 1:10 to plot dims 1 to 10">
                    <validator type="regex" message="Please only use numbers or colon">^[\d:]+$</validator>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VlnPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/VlnPlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test2: FeatureScatter PDF -->
            <param name="seurat_rds" location="https://zenodo.org/records/17817806/files/filtered.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="FeatureScatter"/>
                <param name="feature1" value="nCount_RNA"/>
                <param name="feature2" value="percent.mt"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="FeatureScatter"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/FeatureScatter.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test3: CellScatter PDF -->
            <param name="seurat_rds" location="https://zenodo.org/records/17817806/files/variablefeatures.rds"/>
            <param name="plot_format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="CellScatter"/>
                <param name="cell1" value="X16cell"/>
                <param name="cell2" value="midblast.9"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="CellScatter"/>
                </assert_contents>
            </output>
            <output name="plot_out_pdf" location="https://zenodo.org/records/17817806/files/CellScatter.pdf" ftype="pdf" compare="diff" lines_diff="50"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test4: VariableFeaturePlot SVG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/variablefeatures.rds"/>
            <param name="plot_format" value="svg"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VariableFeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_svg" location="https://zenodo.org/records/17817806/files/VariableFeaturePlot.svg" ftype="svg" compare="diff" lines_diff="50"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test5: VizDimLoadings JPEG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="jpeg"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VizDimLoadings"/>
                </assert_contents>
            </output>
            <output name="plot_out_jpeg" location="https://zenodo.org/records/17817806/files/VizDimLoadings.jpeg" ftype="jpeg" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test6: DimPlot TEX -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/umap.rds"/>
            <param name="plot_format" value="tex"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DimPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_tex" location="https://zenodo.org/records/17817806/files/DimPlot.tex" ftype="tex">
                <assert_contents>
                    <has_text_matching expression="beginpicture"/>
                </assert_contents>
            </output>
        </test>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DimHeatmap"/>
                </assert_contents>
            </output>
            <output name="plot_out_tiff" location="https://zenodo.org/records/17817806/files/DimHeatmap.tiff" ftype="tiff" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test8: ElbowPlot EPS -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="eps"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="ElbowPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_eps" location="https://zenodo.org/records/17817806/files/ElbowPlot.eps" ftype="eps"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test9: FeaturePlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/umap.rds"/>
            <param name="plot_format" value="png"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="FeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/FeaturePlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test10: DoHeatmap PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
            <param name="plot_format" value="png"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DoHeatmap"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/DoHeatmap.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test11: DotPlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
            <param name="plot_format" value="png"/>

            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DotPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/DotPlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test12: ImageDimPlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/17807529/files/test_seurat_spatial.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="fov" value="anterior1"/>
                <param name="method" value="ImageDimPlot"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="ImageDimPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/ImageDimPlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test13: ImageFeaturePlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/17807529/files/test_seurat_spatial.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="ImageFeaturePlot"/>
                <param name="fov" value="anterior1"/>
                <param name="features" value="Xkr4"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="ImageFeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/ImageFeaturePlot.png" ftype="png" compare="image_diff"/>
        </test>
    </tests>
    <help><![CDATA[
Seurat
======