comparison plot.xml @ 7:7647e5cd1b8b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"

6:dbbe1ea8ecb1

sc.pl.scatter(
    @CMD_param_plot_inputs@
    #if $method.type.type == 'xy'
    x='$method.type.x',
    y='$method.type.y',
        #if str('$method.type.layers.use_layers') == 'true'
    layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
        #end if
    #else
    basis='$method.type.basis',

    sort_order=$method.sort_order,
    @CMD_params_groups@
    @CMD_params_pl_components@
    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    @CMD_param_legend_fontsize@
    legend_fontweight='$method.plot.legend_fontweight',
    color_map='$method.plot.color_map',
    #if str($method.plot.palette) != ''
    palette='$method.plot.palette',
    #end if
    frameon=$method.plot.frameon,
    @CMD_param_title@
    @CMD_param_size@)

#else if $method.method == 'pl.heatmap'
sc.pl.heatmap(
    @CMD_param_plot_inputs@
    @CMD_params_inputs@

                    <param name="type" type="select" label="Plotting tool that computed coordinates" help="">
                        <option value="xy">Using coordinates</option>
                        <option value="basis">Using tool that computes coordinates</option>
                    </param>
                    <when value="xy">
                        <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'"/>
                        <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'"/>
                        <conditional name="layers">
                            <param argument="use_layers" type="select" label="Use the layers attribute?">
                                <option value="true">Yes</option>
                                <option value="false" selected="true">No</option>
                            </param>
                            <when value="true">
                                <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present"/>
                                <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present"/>
                                <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present"/>
                            </when>
                            <when value="false"/>
                        </conditional>
                    </when>
                    <when value="basis">

                        <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
                    </param>
                    <when value="var_names"/>
                    <when value="obs"/>
                    <when value="custom">
                        <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'"/>
                    </when>
                </conditional>
                <expand macro="param_groupby"/>
                <expand macro="param_log"/>
                <expand macro="param_use_raw"/>

                        </when>
                        <when value="False"/>
                    </conditional>
                    <expand macro="param_scale"/>
                </section>
                <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None',    otherwise, no label is shown."/>
                <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
                <expand macro="seaborn_violinplot"/>
            </when>
            <when value="pl.stacked_violin">
                <expand macro="params_inputs"/>

                <expand macro="params_inputs"/>
                <expand macro="params_plots"/>
                <expand macro="pl_matrixplot"/>
            </when>
            <when value="pl.clustermap">
                <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/>
                <expand macro="param_use_raw"/>
                <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
                    <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
                        <option value="single">single: Nearest Point Algorithm</option>
                        <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>

                <expand macro="param_log"/>
                <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
            </when>
            <when value="pl.highest_expr_genes">
                <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
                <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'."/>
                <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>

                <expand macro="param_groups"/>
                <expand macro="pl_attribute_section"/>
                <expand macro="section_matplotlib_pyplot_scatter"/>
            </when>
            <when value="pl.pca_loadings">
                <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components"/>
            </when>
            <when value="pl.pca_variance_ratio">
                <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
                <expand macro="param_log"/>
            </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"/>
                <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
                <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups"/>
                <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
                <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
                <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
                <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
                <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/>

                    </param>
                    <when value="n_genes">
                        <expand macro="param_n_genes"/>
                    </when>
                    <when value="gene_names">
                        <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/>
                    </when>
                </conditional>
                <expand macro="gene_symbols"/>
                <expand macro="param_use_raw"/>
                <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>

7:7647e5cd1b8b

sc.pl.scatter(
    @CMD_param_plot_inputs@
    #if $method.type.type == 'xy'
    x='$method.type.x',
    y='$method.type.y',
    #if str($method.type.color) != ''
    color='$method.type.color',
	  #end if
        #if str('$method.type.layers.use_layers') == 'true'
    layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
        #end if
    #else
    basis='$method.type.basis',

    sort_order=$method.sort_order,
    @CMD_params_groups@
    @CMD_params_pl_components@
    projection='$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@
    legend_fontweight='$method.plot.legend_fontweight',
    @CMD_param_title@
    @CMD_param_size@
    frameon=$method.plot.frameon)

#else if $method.method == 'pl.heatmap'
sc.pl.heatmap(
    @CMD_param_plot_inputs@
    @CMD_params_inputs@

                    <param name="type" type="select" label="Plotting tool that computed coordinates" help="">
                        <option value="xy">Using coordinates</option>
                        <option value="basis">Using tool that computes coordinates</option>
                    </param>
                    <when value="xy">
                        <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
                            <expand macro="sanitize_query" />
                        </param>
                        <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
                            <expand macro="sanitize_query" />
                        </param>
                        <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
                            <expand macro="sanitize_query" />
                        </param>
                        <conditional name="layers">
                            <param argument="use_layers" type="select" label="Use the layers attribute?">
                                <option value="true">Yes</option>
                                <option value="false" selected="true">No</option>
                            </param>
                            <when value="true">
                                <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present">
                                    <expand macro="sanitize_query" />
                                </param>
                                <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present">
                                    <expand macro="sanitize_query" />
                                </param>
                                <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present">
                                    <expand macro="sanitize_query" />
                                </param>
                            </when>
                            <when value="false"/>
                        </conditional>
                    </when>
                    <when value="basis">

                        <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
                    </param>
                    <when value="var_names"/>
                    <when value="obs"/>
                    <when value="custom">
                        <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="sanitize_query" />
                        </param>
                    </when>
                </conditional>
                <expand macro="param_groupby"/>
                <expand macro="param_log"/>
                <expand macro="param_use_raw"/>

                        </when>
                        <when value="False"/>
                    </conditional>
                    <expand macro="param_scale"/>
                </section>
                <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None',    otherwise, no label is shown.">
                    <expand macro="sanitize_query" />
                </param>
                <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
                <expand macro="seaborn_violinplot"/>
            </when>
            <when value="pl.stacked_violin">
                <expand macro="params_inputs"/>

                <expand macro="params_inputs"/>
                <expand macro="params_plots"/>
                <expand macro="pl_matrixplot"/>
            </when>
            <when value="pl.clustermap">
                <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">
                    <expand macro="sanitize_query" />
                </param>
                <expand macro="param_use_raw"/>
                <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
                    <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
                        <option value="single">single: Nearest Point Algorithm</option>
                        <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>

                <expand macro="param_log"/>
                <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
            </when>
            <when value="pl.highest_expr_genes">
                <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
                <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'.">
                    <expand macro="sanitize_query" />
                </param>
                <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="">
                        <expand macro="sanitize_query" />
                    </param>
                    <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>

                <expand macro="param_groups"/>
                <expand macro="pl_attribute_section"/>
                <expand macro="section_matplotlib_pyplot_scatter"/>
            </when>
            <when value="pl.pca_loadings">
                <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components">
                    <expand macro="sanitize_query" />
                </param>
            </when>
            <when value="pl.pca_variance_ratio">
                <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
                <expand macro="param_log"/>
            </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">
                    <expand macro="sanitize_query" />
                </param>
                <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="sanitize_query" />
                </param>
                <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="sanitize_query" />
                </param>
                <expand macro="param_color_map"/>
                <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
                <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups">
                    <expand macro="sanitize_query" />
                </param>
                <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
                <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
                <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
                <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
                <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/>

                    </param>
                    <when value="n_genes">
                        <expand macro="param_n_genes"/>
                    </when>
                    <when value="gene_names">
                        <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
                                <expand macro="sanitize_query" />
                        </param>
                    </when>
                </conditional>
                <expand macro="gene_symbols"/>
                <expand macro="param_use_raw"/>
                <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>