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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:56 +0000
parents 5bf8eb50b280
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<tool id="ip_count_objects" name="Count objects in label map" version="0.0.5-2">
    <description></description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command>
    <![CDATA[
        python '$__tool_directory__/count_objects.py' '$input' '$output'
    ]]>
    </command>
    <inputs> 
        <param name="input" type="data" format="tiff,png" label="Source file" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.tiff"/>
            <output name="output" value="table.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool counts objects in a labeled image.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>