annotate imagej2_find_edges.xml @ 2:5023cbf98ca3 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

<tool id="imagej2_find_edges" name="Find edges" version="@WRAPPER_VERSION@.2">
    <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 error_log = '$output_log.txt'
#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 '$__tool_directory__/imagej2_find_edges_jython_script.py'
'$error_log'
'$input_with_ext'
'$output_filename'
'$input.ext'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
else
    mv '$output_filename' '$output';
fi
]]></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="sim_size"/>
        </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>