view split_labelmap.xml @ 2:7a2e2e3cf836 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ commit c045f067a57e8308308cf6329060c7ccd3fc372f

<tool id="ip_split_labelmap" name="Split label map using morphological operators" version="0.2-2">
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
    </creator>
    <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 detect_errors="aggressive"> 
        <![CDATA[
        python '$__tool_directory__/split_labelmap.py' '$input' '$output'
        ]]>
    </command>
    <inputs> 
        <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image containing labels"/> 
    </inputs>
    <outputs>
        <data name="output" format="tiff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="sample_seg.tif"/>
            <expand macro="tests/label_image_diff" name="output" value="out.tif" ftype="tiff"/>
        </test>
    </tests>
    <help>

        **Splits label map using morphological operators.**

        Takes a labeled image and outputs a similar file where the labeled parts
        of the image that touch (or overlap) are separated by at least 1 pixel (at most 2 pixels).

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>