view imagej2_watershed_binary.xml @ 3:29aca8eebdaa draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

<tool id="imagej2_watershed_binary" name="Perform segmentation using watershed transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">imagej</xref>
        <xref type="biii">imagej2</xref>
    </xrefs>
    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
#set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
ln -s '$input.file_name' '$input_with_ext' &&
#set output_filename = '.'.join(['output', $input.ext])
touch '$output_filename' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_watershed_binary_jython_script.py'
'$input_with_ext'
'$black_background'
'$output_filename'
'$input.ext'
&& mv '$output_filename' '$output';
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <expand macro="black_background_param"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <output name="output" file="blobs_watershed_binary.gif" compare="image_diff"/>
        </test>
        <test>
            <param name="input" value="confocal-series-first-channel_threshold_default.tiff"/>
            <param name="black_background" value="yes"/>
            <output name="output" file="confocal-series-first-channel_default_threshold_watershed.tiff" compare="sim_size"/>
        </test>
    </tests>
    <help>
.. class:: warningmark

@requires_binary_input@

**What it does**

<![CDATA[
Watershed segmentation is a way of automatically separating or cutting apart particles that touch.
It first calculates the Euclidian distance map (EDM) and finds the ultimate eroded points (UEPs).
It then dilates each of the UEPs (the peaks or local maxima of the EDM) as far as possible — either
until the edge of the particle is reached, or the edge touches a region of another (growing) UEP.
Watershed segmentation works best for smooth convex objects that don’t overlap too much.
]]>

    </help>
    <expand macro="fiji_headless_citations"/>
</tool>