view imagej2_find_edges.xml @ 3:633bea9c8ee0 draft default tip

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

<tool id="imagej2_find_edges" name="Find edges" 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 '$__tool_directory__/imagej2_find_edges_jython_script.py'
'$input_with_ext'
'$output_filename'
'$input.ext'
&& mv '$output_filename' '$output';
]]></command>
    <inputs>
        <expand macro="param_input"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <output name="output" file="blobs_find_edges.gif" compare="image_diff"/>
        </test>
    </tests>
    <help>

**What it does**

Uses a Sobel edge detector to highlight sharp changes in intensity in the active image.
The two 3x3 convolution kernels shown below are used to generate vertical and horizontal
derivatives.  The final image is produced by combining the two derivatives using the square
root of the sum of the squares.

``1  2  1     1  0 -1``

``0  0  0     2  0 -2``

``-1 -2 -1    1  0 -1``

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