annotate imagej2_sharpen.xml @ 1:4c43ba752312 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

<tool id="imagej2_sharpen" name="Sharpen" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set error_log = 'output_log.txt'
touch '$error_log' &&
#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 '$__tool_directory__/imagej2_sharpen_jython_script.py'
'$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_sharpen.gif" compare="sim_size"/>
        </test>
    </tests>
    <help>

**What it does**

<![CDATA[

Increases contrast and accentuates detail in the image, but may also accentuate noise. This filter
uses the following weighting factors to replace each pixel with a weighted average of the 3x3 neighborhood.

``-1 -1 -1``

``-1 12 -1``

``-1 -1 -1``

]]>

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