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comparison imagej2_macros.xml @ 0:706af1d7028a draft

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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 17:11:26 -0400
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children 5d633d30316e
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-1:000000000000 0:706af1d7028a
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>