annotate imagej2_make_binary.xml @ 0:baa308e2533a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_make_binary" name="Convert to binary" version="@WRAPPER_VERSION@.0">
    <description>(black and white)</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_make_binary.py
    --input "$input"
    --input_datatype $input.ext
    @make_binary_args@
    --jython_script $__tool_directory__/imagej2_make_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="make_binary_params" />
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="clown.jpg" />
            <param name="input_datatype" value="jpg" />
            <param name="iterations" value="1" />
            <param name="count" value="1" />
            <param name="black_background" value="no" />
            <param name="pad_edges_when_eroding" value="no" />
            <param name="output_datatype" value="jpg" />
            <output name="output" file="clown_binary.jpg" compare="sim_size" />
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Converts an image into a binary (black and white) image by analyzing the histogram of
the  entire image and setting an automatic threshold level to create the binary image.

- **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
- **Count** - Specifies the number of adjacent background pixels necessary before a pixel is removed from the edge of an object during erosion and the number of adjacent foreground pixels necessary before a pixel is added to the edge of an object during dilation.
- **Black background** - If **Yes**, binary images will be created without using an inverted LUT and an assumption that the input image contains white objects on a black background will be made.
- **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.

]]>

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