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comparison auto_threshold.xml @ 3:0c777d708acc draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
author imgteam
date Sat, 19 Feb 2022 15:17:40 +0000
parents 4853fc2b50bf
children 3df9f0a4bf34
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2:81f0cbca04a7 3:0c777d708acc
1 <tool id="ip_threshold" name="Auto Threshold" version="0.0.4"> 1 <tool id="ip_threshold" name="Auto Threshold" version="0.0.5" profile="20.05">
2 <description>applies a standard threshold algorithm to an image</description> 2 <description>applies a standard thresholding algorithm to an image</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement> 4 <requirement type="package" version="0.18.1">scikit-image</requirement>
5 <requirement type="package" version="1.15.4">numpy</requirement> 5 <requirement type="package" version="2020.10.1">tifffile</requirement>
6 <requirement type="package" version="5.3.0">pillow</requirement>
7 <requirement type="package" version="0.15.1">tifffile</requirement>
8 </requirements> 6 </requirements>
9 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
10 <![CDATA[ 8 <![CDATA[
11 python '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background 9 python '$__tool_directory__/auto_threshold.py'
10 '$input'
11 ./out.tif
12 '$th_method'
13 '$block_size'
14 '$dark_bg'
12 ]]> 15 ]]>
13 </command> 16 </command>
14 <inputs> 17 <inputs>
15 <param name="input" type="data" format="tiff" label="Source file" /> 18 <param name="input" type="data" format="tiff,png" label="Input image" />
16 <param name="thresh_type" type="select" label="Threshold Algorithm"> 19 <param name="th_method" type="select" label="Thresholding method">
17 <option value="otsu" selected="True">Otsu</option> 20 <option value="otsu" selected="True">Otsu</option>
18 <option value="li">Li’s Minimum Cross Entropy</option> 21 <option value="li">Li's Minimum Cross Entropy</option>
19 <option value="isodata">Isodata</option> 22 <option value="isodata">Isodata</option>
20 <option value="gaussian_adaptive">Adaptive (Gauss)</option>
21 <option value="mean_adaptive">Adaptive (Mean)</option>
22 <option value="yen">Yen</option> 23 <option value="yen">Yen</option>
24 <option value="loc_gaussian">Adaptive (Gaussian)</option>
25 <option value="loc_median">Adaptive (Median)</option>
26 <option value="loc_mean">Adaptive (Mean)</option>
23 </param> 27 </param>
24 <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" /> 28 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold (only valid for adaptive thresholding methods)" />
29 <param name="dark_bg" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
25 </inputs> 30 </inputs>
26 <outputs> 31 <outputs>
27 <data format="tiff" name="output" /> 32 <data format="tiff" name="output" from_work_dir="out.tif" />
28 </outputs> 33 </outputs>
29 <tests> 34 <tests>
30 <test> 35 <test>
31 <param name="input" value="sample.tif"/> 36 <param name="input" value="sample.tif"/>
32 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> 37 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
33 <param name="thresh_type" value="gaussian_adaptive"/> 38 <param name="th_method" value="loc_gaussian"/>
34 <param name="dark_backgroud" value="True"/> 39 <param name="block_size" value="3"/>
40 <param name="dark_bg" value="True"/>
35 </test> 41 </test>
36 <test> 42 <test>
37 <param name="input" value="sample.tif"/> 43 <param name="input" value="sample.tif"/>
38 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/> 44 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
39 <param name="thresh_type" value="otsu"/> 45 <param name="th_method" value="otsu"/>
40 <param name="dark_backgroud" value="True"/> 46 <param name="block_size" value="5"/>
47 <param name="dark_bg" value="True"/>
41 </test> 48 </test>
42 </tests> 49 </tests>
43 <help> 50 <help>
44 Applies a standard threshold algorithm to an image. 51 Applies a standard thresholding algorithm to an image.
45 </help> 52 </help>
46 <citations> 53 <citations>
47 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 54 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
48 </citations> 55 </citations>
49 </tool> 56 </tool>