Mercurial > repos > imgteam > imagej2_binary_to_edm
diff imagej2_binary_to_edm.xml @ 0:f62303e87275 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 16:54:50 -0400 |
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children | 33f6b1f921e7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_binary_to_edm.xml Tue Sep 17 16:54:50 2019 -0400 @@ -0,0 +1,64 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.0"> + <description>(Euclidean Distance Map)</description> + <macros> + <import>imagej2_macros.xml</import> + </macros> + <expand macro="fiji_requirements" /> + <command> +<![CDATA[ + python $__tool_directory__/imagej2_binary_to_edm.py + --input "$input" + --input_datatype $input.ext + @make_binary_args@ + --jython_script $__tool_directory__/imagej2_binary_to_edm_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="blobs.gif" /> + <param name="iterations" value="1" /> + <param name="count" value="1" /> + <output name="output" file="blobs_edm.gif" compare="sim_size" /> + </test> + <test> + <param name="input" value="blobs.gif" /> + <param name="iterations" value="10" /> + <param name="count" value="3" /> + <param name="black_background" value="yes" /> + <param name="pad_edges_when_eroding" value="yes" /> + <output name="output" file="blobs_black_edm.gif" compare="sim_size" /> + </test> + </tests> + <help> + +.. class:: warningmark + +@requires_binary_input@ + +**What it does** + +<![CDATA[ +Converts a binary image into an 8-bit grayscale Euclidean Distance Map (EDM). Each foreground +(nonzero) pixel in the binary image is assigned a value equal to its distance from the nearest +background (zero) pixel. + +- **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>