Mercurial > repos > imgteam > imagej2_make_binary
diff 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"
author | imgteam |
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date | Tue, 17 Sep 2019 17:07:31 -0400 |
parents | |
children | 6e8be21a505c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_make_binary.xml Tue Sep 17 17:07:31 2019 -0400 @@ -0,0 +1,54 @@ +<?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>