Mercurial > repos > imgteam > imagej2_enhance_contrast
comparison imagej2_macros.xml @ 0:edfc597fb180 draft
"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 17:01:04 -0400 |
parents | |
children | ef3de3e84817 |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <macros> | |
3 <token name="@WRAPPER_VERSION@">3.0</token> | |
4 <xml name="fiji_requirements"> | |
5 <requirements> | |
6 <requirement type="package" version="20170530">fiji</requirement> | |
7 </requirements> | |
8 </xml> | |
9 <xml name="stdio"> | |
10 <stdio> | |
11 <exit_code range="1:"/> | |
12 <exit_code range=":-1"/> | |
13 <regex match="Error:"/> | |
14 <regex match="Exception:"/> | |
15 </stdio> | |
16 </xml> | |
17 <xml name="image_type"> | |
18 <param name="image_type" type="select" label="Image type"> | |
19 <option value="8-bit_white" selected="True">8-bit white</option> | |
20 <option value="8-bit_black">8-bit black</option> | |
21 <option value="8-bit_random">8-bit random</option> | |
22 <option value="8-bit_ramp">8-bit ramp</option> | |
23 <option value="16-bit_white">16-bit white</option> | |
24 <option value="16-bit_black">16-bit black</option> | |
25 <option value="16-bit_random">16-bit random</option> | |
26 <option value="16-bit_ramp">16-bit ramp</option> | |
27 <option value="32-bit_white">32-bit white</option> | |
28 <option value="32-bit_black">32-bit black</option> | |
29 <option value="32-bit_random">32-bit random</option> | |
30 <option value="32-bit_ramp">32-bit ramp</option> | |
31 <option value="RGB_white">RGB white</option> | |
32 <option value="RGB_black">RGB black</option> | |
33 <option value="RGB_random">RGB random</option> | |
34 <option value="RGB_ramp">RGB ramp</option> | |
35 </param> | |
36 </xml> | |
37 <xml name="make_binary_params"> | |
38 <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/> | |
39 <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/> | |
40 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite)."> | |
41 <option value="no" selected="True">No</option> | |
42 <option value="yes">Yes</option> | |
43 </param> | |
44 <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image."> | |
45 <option value="no" selected="True">No</option> | |
46 <option value="yes">Yes</option> | |
47 </param> | |
48 </xml> | |
49 <xml name="black_background_param"> | |
50 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite)."> | |
51 <option value="no" selected="True">No</option> | |
52 <option value="yes">Yes</option> | |
53 </param> | |
54 </xml> | |
55 <token name="@make_binary_args@"> | |
56 --iterations $iterations | |
57 --count $count | |
58 --black_background $black_background | |
59 --pad_edges_when_eroding $pad_edges_when_eroding | |
60 </token> | |
61 <token name="@requires_binary_input@"> | |
62 .. class:: warningmark | |
63 | |
64 This tool works on binary images, so other image types will automatically be converted to binary | |
65 before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with | |
66 the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool | |
67 allows you to choose the **Black background** setting. If these settings are not appropriate, | |
68 first manually convert the image to binary using the **Convert to binary (black and white)** | |
69 tool, which allows you to change them. | |
70 </token> | |
71 <xml name="image_datatypes"> | |
72 <option value="bmp">bmp</option> | |
73 <option value="gif">gif</option> | |
74 <option value="jpg">jpg</option> | |
75 <option value="png" selected="true">png</option> | |
76 <option value="tiff">tiff</option> | |
77 </xml> | |
78 <xml name="bunwarpj_citations"> | |
79 <citations> | |
80 <citation type="bibtex"> | |
81 @InProceedings(Arganda-Carreras2006, | |
82 author = "Ignacio Arganda-Carreras and | |
83 Carlos Oscar S{\'a}nchez Sorzano and | |
84 Roberto Marabini and | |
85 Jos{\'e} Mar\'{\i}a Carazo and | |
86 Carlos Ortiz-de-Solorzano and | |
87 Jan Kybic", | |
88 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization", | |
89 publisher = "Springer Berlin / Heidelberg", | |
90 booktitle = "Computer Vision Approaches to Medical Image Analysis", | |
91 series = "Lecture Notes in Computer Science", | |
92 year = "2006", | |
93 volume = "4241", | |
94 pages = "85-95", | |
95 month = "May", | |
96 city = "Graz, Austria") | |
97 </citation> | |
98 <citation type="doi">10.1038/nmeth.2019</citation> | |
99 </citations> | |
100 </xml> | |
101 <xml name="fiji_headless_citations"> | |
102 <citations> | |
103 <citation type="doi">10.1038/nmeth.2102</citation> | |
104 </citations> | |
105 </xml> | |
106 </macros> |