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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
author iuc
date Sat, 09 Feb 2019 11:24:40 -0500
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1 <tool id="ip_threshold" name="Auto Threshold" version="0.0.3">
2 <description>applies a standard threshold algorithm to an image</description>
3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="1.15.4">numpy</requirement>
6 <requirement type="package" version="5.3.0">pillow</requirement>
7 <requirement type="package" version="0.15.1">tifffile</requirement>
8 </requirements>
9 <command detect_errors="aggressive">
10 <![CDATA[
11 python '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background
12 ]]>
13 </command>
14 <inputs>
15 <param name="input" type="data" format="tiff" label="Source file" />
16 <param name="thresh_type" type="select" label="Threshold Algorithm">
17 <option value="otsu" selected="True">Otsu</option>
18 <option value="li">Li’s Minimum Cross Entropy</option>
19 <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 </param>
24 <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
25 </inputs>
26 <outputs>
27 <data format="tiff" name="output" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="input" value="sample.tif"/>
32 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
33 <param name="thresh_type" value="gaussian_adaptive"/>
34 <param name="dark_backgroud" value="True"/>
35 </test>
36 <test>
37 <param name="input" value="sample.tif"/>
38 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
39 <param name="thresh_type" value="otsu"/>
40 <param name="dark_backgroud" value="True"/>
41 </test>
42 </tests>
43 <help>
44 Applies a standard threshold algorithm to an image.
45 </help>
46 <citations>
47 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
48 </citations>
49 </tool>