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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
author imgteam
date Thu, 06 Mar 2025 18:12:13 +0000
parents 29110ca1b63a
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1:29110ca1b63a 2:387414aa6496
1 <tool id="ip_color_deconvolution" name="Color Deconvolution" version="0.8">
2 <description>Color deconvolution</description>
3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="4.0.0">pillow</requirement>
6 <requirement type="package" version="0.18.1">scikit-learn</requirement>
7 <requirement type="package" version="1.12">numpy</requirement>
8 <requirement type="package" version="0.15.1">tifffile</requirement>
9 </requirements>
10 <command detect_errors="aggressive">
11 <![CDATA[
12 python '$__tool_directory__/color_deconvolution.py' '$input' '$output' '$convtype'
13 ]]>
14 </command>
15 <inputs>
16 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file with 3 channels"/>
17 <param name="convtype" type="select" label="Transformation type">
18 <option value="ica" selected="True">ica</option>
19 <option value="pca">pca</option>
20 <option value="nmf">nmf</option>
21 <option value="fa">fa</option>
22 <option value="xyz2rgb">xyz2rgb</option>
23 <option value="rgb_from_rbd">rgb_from_rbd</option>
24 <option value="rgb_from_hdx">rgb_from_hdx</option>
25 <option value="rgb2hsv">rgb2hsv</option>
26 <option value="rgb_from_bro">rgb_from_bro</option>
27 <option value="bpx_from_rgb">bpx_from_rgb</option>
28 <option value="hed_from_rgb">hed_from_rgb</option>
29 <option value="rgbcie2rgb">rgbcie2rgb</option>
30 <option value="hdx_from_rgb">hdx_from_rgb</option>
31 <option value="xyz2luv">xyz2luv</option>
32 <option value="rgb2lab">rgb2lab</option>
33 <option value="hpx_from_rgb">hpx_from_rgb</option>
34 <option value="rgb_from_fgx">rgb_from_fgx</option>
35 <option value="rgb_from_gdx">rgb_from_gdx</option>
36 <option value="lab2xyz">lab2xyz</option>
37 <option value="rgb_from_hpx">rgb_from_hpx</option>
38 <option value="lab2rgb">lab2rgb</option>
39 <option value="rgb2rgbcie">rgb2rgbcie</option>
40 <option value="bex_from_rgb">bex_from_rgb</option>
41 <option value="xyz2lab">xyz2lab</option>
42 <option value="rgb_from_bex">rgb_from_bex</option>
43 <option value="fgx_from_rgb">fgx_from_rgb</option>
44 <option value="rbd_from_rgb">rbd_from_rgb</option>
45 <option value="rgb2hed">rgb2hed</option>
46 <option value="hed2rgb">hed2rgb</option>
47 <option value="luv2rgb">luv2rgb</option>
48 <option value="luv2xyz">luv2xyz</option>
49 <option value="lch2lab">lch2lab</option>
50 <option value="rgb2luv">rgb2luv</option>
51 <option value="ahx_from_rgb">ahx_from_rgb</option>
52 <option value="rgb_from_hax">rgb_from_hax</option>
53 <option value="hax_from_rgb">hax_from_rgb</option>
54 <option value="rgb_from_bpx">rgb_from_bpx</option>
55 <option value="rgb2xyz">rgb2xyz</option>
56 <option value="gdx_from_rgb">gdx_from_rgb</option>
57 <option value="rgb_from_ahx">rgb_from_ahx</option>
58 <option value="lab2lch">lab2lch</option>
59 <option value="rgb_from_hed">rgb_from_hed</option>
60 <option value="bro_from_rgb">bro_from_rgb</option>
61 <option value="hsv2rgb">hsv2rgb</option>
62 </param>
63 </inputs>
64 <outputs>
65 <data format="tiff" name="output"/>
66 </outputs>
67 <tests>
68 <test>
69 <param name="input" value="galaxyIcon_noText.png" />
70 <param name="convtype" value="rgb2hsv" />
71 <output name="output" ftype="tiff" />
72 </test>
73 </tests>
74 <help>
75 **What it does**
76
77 This tools performs several color deconvolution techniques.</help>
78 <citations>
79 <citation type="doi">10.7717/peerj.453</citation>
80 <citation type="bibtex">@inproceedings{sklearn_api,
81 author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
82 Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
83 Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
84 and Jaques Grobler and Robert Layton and Jake VanderPlas and
85 Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
86 title = {{API} design for machine learning software: experiences from the scikit-learn
87 project},
88 booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
89 year = {2013},
90 pages = {108--122},
91 }</citation>
92 </citations>
93 </tool>