view squidpy_scatter.xml @ 0:6fe0d4f464f4 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 721eaced787aa3b04d96ad91f6b4540f26b23949

<tool id="squidpy_scatter" name="Create spatial scatterplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>with Squidpy</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <expand macro="squidpy_requirements"/>
    <expand macro="macro_stdio" />
    <version_command>echo "@TOOL_VERSION@"</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
        export TQDM_DISABLE=True &&
        python '$__tool_directory__/squidpy_scatter.py'
            --inputs '$inputs'
            --output_plot image.png
        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
        <param name="x_coord" type="text" value="X_centroid" label="Key for X spatial coordinate in adata.obs" />
        <param name="y_coord" type="text" value="Y_centroid" label="Key for Y spatial coordinate in adata.obs" />
        <param argument="color" type="text" value="phenotype" label="Key for annotations in adata.obs or variables/genes" />
        <section name="plot_opts" title="Advanced Plot Options" expanded="false">
            <param argument="groups" type="text" optional="true" label="For discrete annotation in color, select which values to plot" />
            <param argument="use_raw" type="boolean" checked="false" label="Use adata.raw.X instead of adata.X" />
            <param argument="crop_coord" type="text" optional="true" label="Coordinates to crop scatterplot by" help="x1,y1,x2,y2" />
        </section>
        <section name="legend_opts" title="Legend Options" expanded="false">
            <param argument="legend_loc" type="text" value="right margin" optional="true" label="Location of the legend" />
            <param argument="legend_fontsize" type="integer" value="8" optional="true" label="Font size for the legend" />
            <param argument="legend_fontweight" type="text" value="bold" optional="true" label="Font weight for the legend" />
            <param argument="legend_fontoutline" type="integer" value="" optional="true" label="Font outline for the legend" />
            <param argument="legend_na" type="boolean" checked="true" label="Show NA values in the legend" />
        </section>
        <section name="aesthetic_opts" title="Figure Aesthetic Options" expanded="false">
            <param argument="size" type="integer" value="3" label="Size of the scatter point/shape" />
            <param argument="alpha" type="float" min="0.01" max="1.0" value="1.0" label="Alpha value for scatter point/shape" />
            <param argument="cmap" type="text" value="viridis" optional="true" label="Matplotlib colormap for continuous annotations" help="Refer to `matplotlib.pyplot.cmap`." />
            <param argument="colorbar" type="boolean" checked="true" label="Show the colorbar" />
            <param argument="scalebar_dx" type="float" min="0.01" max="1.0" value="" optional="true" label="Size of one pixel in units specified by scalebar_units" />
            <param argument="scalebar_units" type="text" value="" optional="true" label="Units for scalebar" />
            <param argument="title" type="text" optional="true" label="Figure title" />
            <param argument="figsize" type="text" value="" optional="true" label="Size of the figure in inches" help="width,height"/>
            <param argument="dpi" type="integer" value="300" optional="true" label="Dots per inch" />
        </section>
    </inputs>
    <outputs>
        <data from_work_dir="figures/image.png" format="png" name="output_plot" label="Squidpy spatial scatterplot on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
            <param name="color" value="cell type" />
            <output name="output_plot" file="scatter_image.png" compare="sim_size" delta="2000" />
        </test>
    </tests>
    <help>
        <![CDATA[
This is a limited implementation of the squidpy.pl.spatial_scatter() function 

See Squidpy documentation for more information: 

https://squidpy.readthedocs.io/en/stable/index.html
        ]]>
    </help>
    <expand macro="citations" />
</tool>