annotate main_macros.xml @ 1:b84c324b58bd draft default tip

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit ed118f79326f83eff1315f735b4e0e1a45a5e02c

<macros>
    <token name="@TOOL_VERSION@">1.5.0</token>
    <token name="@PROFILE@">20.01</token>
    <token name="@VERSION_SUFFIX@">2</token> 

    <xml name="macro_stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        </stdio>
    </xml>

    <xml name="squidpy_requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">squidpy</requirement>
        </requirements>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41592-021-01358-2</citation>
        </citations>
    </xml>

    <xml name="squidpy_spatial_options">
        <section name="options" title="Advanced Graph Options" expanded="false">
            <yield/>
             <!-- <param argument="copy" type="hidden" value="false" help="If True, return the result, otherwise save it to the adata object." /> -->
        </section>
    </xml>

    <xml name="squidpy_plotting_options">
        <section name="plotting_options" title="Plotting Options" expanded="false">
            <yield />
            <!-- <param argument="legend_kwargs" type="text" value="" optional="true" label="Keyword arguments for matplotlib.pyplot.legend()" /> -->
            <param argument="figsize" type="text" value="" optional="true" label="Size of the figure in inches" help="Optional. e.g.: (12, 12)." />
            <param argument="dpi" type="integer" value="" optional="true" label="Dots per inch" help="Optional" />
        </section>
    </xml>

    <xml name="squidpy_plotting_option_palette">
        <param argument="palette" type="text" value="" optional="true" label="Categorical colormap for the clusters" help="Comma delimited for multiple. If None, use anndata.AnnData.uns ['{cluster_key}_colors'], if available." />
    </xml>

    <xml name="squidpy_plotting_options_more">
        <expand macro="squidpy_plotting_options">
            <yield />
            <param argument="annotate" type="boolean" checked="false" label="Whether to annotate the cells of the heatmap?" />
            <param argument="method" type="select" label="The linkage method to be used for dendrogram/clustering" help="see scipy.cluster.hierarchy.linkage().">
                <option value="none" selected="true">None</option>
                <option value="single">single</option>
                <option value="complete">complete</option>
                <option value="average">average</option>
                <option value="weighted">weighted</option>
                <option value="centroid">centroid</option>
                <option value="median">median</option>
                <option value="ward">ward</option>
            </param>
            <param argument="title" type="text" value="" optional="true" label="The title of the plot" help="Optional." />
            <param argument="cmap" type="text" value="viridis" label="Continuous colormap to use" help="Refer to `matplotlib.pyplot.cmap`." />
            <!-- <param argument="cbar_kwargs" type="text" value="" label="Keyword arguments for matplotlib.figure.Figure.colorbar()" /> -->
            <expand macro="squidpy_plotting_option_palette" />
        </expand>
    </xml>
</macros>