annotate scale_cell_coordinates.xml @ 0:8969e16f3701 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43

<tool id="scale_cell_coordinates" name="Scale cell coordinates" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/scale_cell_coordinates.py'
            --inputs '$inputs'
            --output '$output'
        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="anndata" type="data" format="h5ad" label="Input anndata file" />
        <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 name="resolution" type="float" value="" min="0.01" max="1.0" label="Value to multiply pixel coordinates by" help="Units would be target_unit/pixel (Example: um/pixel)" />
        <param name="unit" type="text" value="um" optional="true" label="Unit for scaled coordinates" help="Will be appended to new column name (Example: 'X_centroid_um')" />
    </inputs>
    <outputs>
        <data format="h5ad" name="output" label="Cell coordinate scaling on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="anndata" value="pixels.h5ad" />
            <param name="resolution" value="0.65" />
            <output name="output" ftype="h5ad">
                <assert_contents>
                    <has_h5_keys keys="obs/X_centroid_um,obs/Y_centroid_um" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[

This tool allows a user to scale x,y pixel coordinates to the physical distance (microns, for example)

**Inputs**
- anndata h5ad file with x,y coordinates in pixels 
- column names for pixel coordinates in adata.obs 
- Physical resolution of the image (microns per pixel, for example)
- Unit for the resulting physical distance ('um', for example)

**Outputs**
- anndata h5ad file with new columns, with column names formatted with 
the existing column name and physical distance appended ('X_centroid_um', for example)

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