view wsi_extract_top_view.xml @ 2:3bd767eee603 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

<tool id="ip_wsi_extract_top_view" name="Extract top view from whole-slide image" version="0.2-2"> 
    <description>with OpenSlide</description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <requirements>  
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="1.1.1">openslide-python</requirement>
        <requirement type="package" version="0.5">glob2</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive"> 
        <![CDATA[
        python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output'
        ]]>
    </command>
    <inputs> 
        <param name="input" type="data" format="svs,svslide,vms,mrxs,tif,tiff" label="Whole Slice Image"/><!--formats taken as listed on https://openslide.org/api/python/-->
    </inputs>
    <outputs>
        <data name="output" format="tiff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="CMU-1-Small-Region.svs"/>
            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
        </test>
    </tests>
    <help>
    **What it does**

    Extracts the top view from a whole-slide image, also known as virtual slide, which are high-resolution images used in digital pathology.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>