comparison imagej2_watershed_binary.xml @ 1:5b154339fd90 draft

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

0:b143159845b4

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.0">
    <description>of binary image</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_watershed_binary.py
    --input "$input"
    --input_datatype $input.ext
    --black_background $black_background
    --jython_script $__tool_directory__/imagej2_watershed_binary_jython_script.py
    --output_datatype $output.ext
    --output "$output"
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
        <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="sim_size" />
        </test>
    </tests>
    <help>
.. class:: warningmark

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>

1:5b154339fd90

<tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.1">
    <description>of binary image</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 '$__tool_directory__/imagej2_watershed_binary_jython_script.py'
'$error_log'
'$input_with_ext'
'$black_background'
'$output_filename'
'$input.ext'
&>'$error_log';
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
else
    mv '$output_filename' '$output';
fi
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <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="sim_size"/>
        </test>
    </tests>
    <help>
.. class:: warningmark

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>