annotate imagej2_shadows.xml @ 2:f3c9192bd0b9 draft default tip

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

<tool id="imagej2_shadows" name="Add shadow effect" 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'
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 '$__tool_directory__/imagej2_shadows_jython_script.py'
'$error_log'
'$input_with_ext'
'$direction'
'$output_filename'
'$input.ext'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
else
    mv '$output_filename' '$output';
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <param name="direction" type="select" label="Direction" help="Light will appear to come from the selected direction">
            <option value="East" selected="True">East</option>
            <option value="North">North</option>
            <option value="Northeast">Northeast</option>
            <option value="Northwest">Northwest</option>
            <option value="South">South</option>
            <option value="Southeast">Southeast</option>
            <option value="Southwest">Southwest</option>
            <option value="West">West</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="direction" value="Northwest"/>
            <output name="output" file="blobs_northwest.gif" compare="sim_size"/>
        </test>
    </tests>
    <help>

**What it does**

<![CDATA[

Produces a shadow effect, with light appearing to come from the selected direction (East, North, Northeast,
Northwest, South, Southeast, Southwest and West). The underlying commands use Convolve 3 × 3, ImageJ’s 3 × 3
convolution function.

]]>

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