annotate tiling_pyhist.xml @ 0:c051e9688932 draft default tip

planemo upload for repository https://github.com/goeckslab/gleam.git commit 11356473f09dd54d86af28b74bd9ed097d07ca04

<tool id="tiling_pyhist" name="Tile Images with PyHIST" version="1.0.0">
    <description>Tile pathology images using PyHIST in parallel</description>

    <requirements>
        <container type="docker">quay.io/goeckslab/galaxy-tiler:1.0.0</container>
    </requirements>
    <stdio>
        <exit_code range="137" level="fatal_oom" description="Out of Memory" />
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>
    <command><![CDATA[
        python "$__tool_directory__/tiling_pyhist.py"
        #for $i, $img in enumerate($input_collection)
            --input '${img}' --original_name "${img.element_identifier}"
        #end for
        --output_zip '$output_zip'
    ]]></command>

    <inputs>
        <param name="input_collection" type="data_collection" collection_type="list" format="svs,tiff,tif" label="Input Image Collection"
               help="Provide a dataset collection of pathology images (.svs, .tiff, .tif)." />
    </inputs>

    <outputs>
        <data name="output_zip" format="zip" label="Image Tiles (zip)" />
    </outputs>
    <tests>
        <test>
            <param name="input_collection">
                <collection type="list">
                    <element name="sample1" ftype="svs" value="CMU-1-Small-Region.svs" />
                </collection>
            </param>
            <output name="output_zip" file="expected_output_CMU-1-Small-Region.zip" compare="sim_size" delta="10000"/>
        </test>
    </tests>
    <help><![CDATA[
        **Tile Images with PyHIST**

        This tool tiles pathology images using PyHIST in parallel using Docker. It accepts a **collection** of pathology images:

        - A dataset collection of individual pathology images (e.g., `.svs`, `.tiff`, `.tif`).

        Each image in the collection will be processed in a batch using PyHIST. The output is a ZIP file containing tiled image folders named after the input images.

        **Inputs:**
        - **Input Image Collection**: Provide a collection of images to tile.
        - **Output ZIP Filename**: The resulting ZIP file of tiled patches.

        **Outputs:**
        - **Tiled Images ZIP**: A single ZIP archive with all tiled outputs.

        **Note**: Requires Docker on the Galaxy server. Ensure sufficient disk and CPU resources for parallel processing.
    ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1008349</citation>
    </citations>
</tool>