Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw

comparison imagej2_macros.xml @ 1:7f9840d3b7e7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:48:49 +0000
parents 95fb6fa70c2f
children bd2aadf0f589
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0:95fb6fa70c2f 1:7f9840d3b7e7
1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros> 1 <macros>
3 <token name="@WRAPPER_VERSION@">3.0</token> 2 <token name="@WRAPPER_VERSION@">3.0</token>
4 <xml name="fiji_requirements"> 3 <xml name="fiji_requirements">
5 <requirements> 4 <requirements>
6 <requirement type="package" version="20170530">fiji</requirement> 5 <requirement type="package" version="20170530">fiji</requirement>
6 <requirement type="package" version="3.4">grep</requirement>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 <xml name="stdio"> 9 <xml name="stdio">
10 <stdio> 10 <stdio>
11 <exit_code range="1:"/> 11 <exit_code range="1:"/>
14 <regex match="Exception:"/> 14 <regex match="Exception:"/>
15 </stdio> 15 </stdio>
16 </xml> 16 </xml>
17 <xml name="image_type"> 17 <xml name="image_type">
18 <param name="image_type" type="select" label="Image type"> 18 <param name="image_type" type="select" label="Image type">
19 <option value="8-bit_white" selected="True">8-bit white</option> 19 <option value="8-bit_white" selected="true">8-bit white</option>
20 <option value="8-bit_black">8-bit black</option> 20 <option value="8-bit_black">8-bit black</option>
21 <option value="8-bit_random">8-bit random</option> 21 <option value="8-bit_random">8-bit random</option>
22 <option value="8-bit_ramp">8-bit ramp</option> 22 <option value="8-bit_ramp">8-bit ramp</option>
23 <option value="16-bit_white">16-bit white</option> 23 <option value="16-bit_white">16-bit white</option>
24 <option value="16-bit_black">16-bit black</option> 24 <option value="16-bit_black">16-bit black</option>
36 </xml> 36 </xml>
37 <xml name="make_binary_params"> 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."/> 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."/> 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)."> 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> 41 <option value="no" selected="true">No</option>
42 <option value="yes">Yes</option> 42 <option value="yes">Yes</option>
43 </param> 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."> 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> 45 <option value="no" selected="true">No</option>
46 <option value="yes">Yes</option> 46 <option value="yes">Yes</option>
47 </param> 47 </param>
48 </xml> 48 </xml>
49 <xml name="black_background_param"> 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)."> 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> 51 <option value="no" selected="true">No</option>
52 <option value="yes">Yes</option> 52 <option value="yes">Yes</option>
53 </param> 53 </param>
54 </xml>
55 <xml name="param_input">
56 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
57 </xml>
58 <xml name="param_source_image">
59 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
60 </xml>
61 <xml name="param_source_mask">
62 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source mask"/>
63 </xml>
64 <xml name="param_target_image">
65 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
66 </xml>
67 <xml name="param_target_mask">
68 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_mask" type="data" label="Target mask"/>
69 </xml>
70 <xml name="test_bunwarpj_raw_transform">
71 <param name="target_image" value="dotblot.jpg"/>
72 <param name="source_image" value="blobs.gif"/>
73 <param name="target_raw_transformation" value="target_raw_transformation.txt"/>
74 <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
75 </xml>
76 <xml name="test_target_source_images">
77 <param name="target_image" value="dotblot.jpg"/>
78 <param name="source_image" value="blobs.gif"/>
54 </xml> 79 </xml>
55 <token name="@make_binary_args@"> 80 <token name="@make_binary_args@">
56 --iterations $iterations 81 --iterations $iterations
57 --count $count 82 --count $count
58 --black_background $black_background 83 --black_background $black_background