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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:52 +0000
parents 02a686fc1654
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<tool id="ip_coordinates_of_roi" name="Convert binary image to points (point coordinates)" version="0.0.4-2">
    <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="0.23.4">pandas</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            python '$__tool_directory__/coordinates_of_roi.py'
            '$im'
            '$pixel_table' 
            $white_obj
            --threshold $threshold
        ]]>
    </command>
    <inputs>
        <param name="im" type="data" format="png" label="Source file" />
        <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false"
            label="Set to Yes if object is white and background black, otherwise set to No" />
        <param name="threshold" type="float" value="0.5" label="Threshold value" />
    </inputs>
    <outputs>
       <data format="tabular" name="pixel_table" />
    </outputs>
    <tests>
        <test>
            <param name="im" value="test.png"/>
            <param name="white_obj" value="true"/>
            <output name="pixel_table" value="newtable.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI).
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>