comparison scimap_plotting.xml @ 2:ef73596d678a draft default tip

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d

1:c42e97dc5a3a

                <section name="options" title="Advanced Options" expanded="false">
                    <param argument="subset_xaxis" type="text" value="" optional="true" label="Subset x-axis prior to plotting. Type in a list of categories to include on x-axis" help="Optional. Comma delimited. Default is all categories in x-axis variable" />
                    <param argument="subset_yaxis" type="text" value="" optional="true" label="Subset y-axis prior to plotting. Type in a list of categories to include on y-axis" help="Optional. Comma delimited. Default is all categories in y-axis variable" />
                    <param argument="order_xaxis" type="text" value="" optional="true" label="Type in a list of categories to order to x-axis" help="Optional. Comma delimited. Default ordering is alphabetical" />
                    <param argument="order_yaxis" type="text" value="" optional="true" label="Type in a list of categories to order to y-axis" help="Optional. Comma delimited. Default ordering is alphabetical" />
                </section>
            </when>
            <when value="voronoi">
                <param argument="color_by" type="text" value="phenotype" optional="false" label="Pass the name of the categorical variable by which to color the voronoi diagram" />
                <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Pass the name of the column containing cell X coordinates" />

    </tests>
    <help>
        <![CDATA[
**What it does**

This tool does various single cell spatial analyses with Scimap.

**Input**

AnnData.

**Output**

Anndata with a corresponding key added.


        ]]>
    </help>
    <expand macro="citations" />
</tool>

2:ef73596d678a

                <section name="options" title="Advanced Options" expanded="false">
                    <param argument="subset_xaxis" type="text" value="" optional="true" label="Subset x-axis prior to plotting. Type in a list of categories to include on x-axis" help="Optional. Comma delimited. Default is all categories in x-axis variable" />
                    <param argument="subset_yaxis" type="text" value="" optional="true" label="Subset y-axis prior to plotting. Type in a list of categories to include on y-axis" help="Optional. Comma delimited. Default is all categories in y-axis variable" />
                    <param argument="order_xaxis" type="text" value="" optional="true" label="Type in a list of categories to order to x-axis" help="Optional. Comma delimited. Default ordering is alphabetical" />
                    <param argument="order_yaxis" type="text" value="" optional="true" label="Type in a list of categories to order to y-axis" help="Optional. Comma delimited. Default ordering is alphabetical" />
                    <param argument="matplotlib_cmap" type="select" label="Matplotlib colormap to use for y-axis categories" help="See link below for colormaps explanation">
                        <option value="Pastel1">Pastel1</option>
                        <option value="Pastel2">Pastel2</option>
                        <option value="Paired">Paired</option>
                        <option value="Accent">Accent</option>
                        <option value="Dark2">Dark2</option>
                        <option selected="true" value="Set1">Set1</option>
                        <option value="Set2">Set2</option>
                        <option value="Set3">Set3</option>
                        <option value="tab10">tab10</option>
                        <option value="tab20">tab20</option>
                        <option value="tab20b">tab20b</option>
                        <option value="tab20c">tab20c</option>
                    </param>
                </section>
            </when>
            <when value="voronoi">
                <param argument="color_by" type="text" value="phenotype" optional="false" label="Pass the name of the categorical variable by which to color the voronoi diagram" />
                <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Pass the name of the column containing cell X coordinates" />

    </tests>
    <help>
        <![CDATA[
**What it does**

This tool creates stacked barplots or Voronoi plots from single-cell spatial data using Scimap

For the stacked barplot tool, find colormap descriptions here: https://matplotlib.org/stable/users/explain/colors/colormaps.html

        ]]>
    </help>
    <expand macro="citations" />
</tool>