Mercurial > repos > imgteam > imagej2_binary_to_edm
comparison imagej2_binary_to_edm.xml @ 0:308625693e9a draft default tip
"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 16:37:50 -0400 |
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| -1:000000000000 | 0:308625693e9a |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>(Euclidean Distance Map)</description> | |
| 4 <macros> | |
| 5 <import>imagej2_macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="fiji_requirements" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 python $__tool_directory__/imagej2_binary_to_edm.py | |
| 11 --input "$input" | |
| 12 --input_datatype $input.ext | |
| 13 @make_binary_args@ | |
| 14 --jython_script $__tool_directory__/imagej2_binary_to_edm_jython_script.py | |
| 15 --output_datatype $output.ext | |
| 16 --output "$output" | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> | |
| 21 <expand macro="make_binary_params" /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="input" value="blobs.gif" /> | |
| 29 <param name="iterations" value="1" /> | |
| 30 <param name="count" value="1" /> | |
| 31 <output name="output" file="blobs_edm.gif" compare="sim_size" /> | |
| 32 </test> | |
| 33 <test> | |
| 34 <param name="input" value="blobs.gif" /> | |
| 35 <param name="iterations" value="10" /> | |
| 36 <param name="count" value="3" /> | |
| 37 <param name="black_background" value="yes" /> | |
| 38 <param name="pad_edges_when_eroding" value="yes" /> | |
| 39 <output name="output" file="blobs_black_edm.gif" compare="sim_size" /> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help> | |
| 43 | |
| 44 .. class:: warningmark | |
| 45 | |
| 46 @requires_binary_input@ | |
| 47 | |
| 48 **What it does** | |
| 49 | |
| 50 <![CDATA[ | |
| 51 Converts a binary image into an 8-bit grayscale Euclidean Distance Map (EDM). Each foreground | |
| 52 (nonzero) pixel in the binary image is assigned a value equal to its distance from the nearest | |
| 53 background (zero) pixel. | |
| 54 | |
| 55 - **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed. | |
| 56 - **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. | |
| 57 - **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. | |
| 58 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image. | |
| 59 | |
| 60 ]]> | |
| 61 | |
| 62 </help> | |
| 63 <expand macro="fiji_headless_citations" /> | |
| 64 </tool> |