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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 17:03:06 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_make_binary" name="Convert to binary" version="@WRAPPER_VERSION@.0">
3 <description>(black and white)</description>
4 <macros>
5 <import>imagej2_macros.xml</import>
6 </macros>
7 <expand macro="fiji_requirements" />
8 <command>
9 <![CDATA[
10 python $__tool_directory__/imagej2_make_binary.py
11 --input "$input"
12 --input_datatype $input.ext
13 @make_binary_args@
14 --jython_script $__tool_directory__/imagej2_make_binary_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="clown.jpg" />
29 <param name="input_datatype" value="jpg" />
30 <param name="iterations" value="1" />
31 <param name="count" value="1" />
32 <param name="black_background" value="no" />
33 <param name="pad_edges_when_eroding" value="no" />
34 <param name="output_datatype" value="jpg" />
35 <output name="output" file="clown_binary.jpg" compare="sim_size" />
36 </test>
37 </tests>
38 <help>
39 **What it does**
40
41 <![CDATA[
42 Converts an image into a binary (black and white) image by analyzing the histogram of
43 the entire image and setting an automatic threshold level to create the binary image.
44
45 - **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
46 - **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.
47 - **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.
48 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
49
50 ]]>
51
52 </help>
53 <expand macro="fiji_headless_citations" />
54 </tool>