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planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
author iuc
date Tue, 04 Aug 2015 13:20:29 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <xml name="fiji_20141125_requirements">
4 <requirements>
5 <requirement type="package" version="20141125">fiji</requirement>
6 </requirements>
7 </xml>
8 <xml name="python_bioformats_104_requirements">
9 <requirements>
10 <requirement type="package" version="20141125">fiji</requirement>
11 <requirement type="package" version="1.0.11">javabridge</requirement>
12 <requirement type="package" version="1.9">numpy</requirement>
13 <requirement type="package" version="1.0.4">python_bioformats</requirement>
14 </requirements>
15 </xml>
16 <xml name="stdio">
17 <stdio>
18 <exit_code range="1:"/>
19 <exit_code range=":-1"/>
20 <regex match="Error:"/>
21 <regex match="Exception:"/>
22 </stdio>
23 </xml>
24 <xml name="image_type">
25 <param name="image_type" type="select" label="Image type">
26 <option value="8-bit_white" selected="True">8-bit white</option>
27 <option value="8-bit_black">8-bit black</option>
28 <option value="8-bit_random">8-bit random</option>
29 <option value="8-bit_ramp">8-bit ramp</option>
30 <option value="16-bit_white">16-bit white</option>
31 <option value="16-bit_black">16-bit black</option>
32 <option value="16-bit_random">16-bit random</option>
33 <option value="16-bit_ramp">16-bit ramp</option>
34 <option value="32-bit_white">32-bit white</option>
35 <option value="32-bit_black">32-bit black</option>
36 <option value="32-bit_random">32-bit random</option>
37 <option value="32-bit_ramp">32-bit ramp</option>
38 <option value="RGB_white">RGB white</option>
39 <option value="RGB_black">RGB black</option>
40 <option value="RGB_random">RGB random</option>
41 <option value="RGB_ramp">RGB ramp</option>
42 </param>
43 </xml>
44 <xml name="make_binary_params">
45 <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."/>
46 <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."/>
47 <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).">
48 <option value="no" selected="True">No</option>
49 <option value="yes">Yes</option>
50 </param>
51 <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.">
52 <option value="no" selected="True">No</option>
53 <option value="yes">Yes</option>
54 </param>
55 </xml>
56 <token name="@make_binary_args@">
57 --iterations $iterations
58 --count $count
59 --black_background $black_background
60 --pad_edges_when_eroding $pad_edges_when_eroding
61 </token>
62 <xml name="max_heap_size_type_conditional">
63 <conditional name="set_max_heap_size">
64 <param name="max_heap_size_type" type="select" label="Maximum size of the memory allocation pool used by the JVM" help="This value must be a multiple of 1024 or it will be ignored and the system default will be used.">
65 <option value="default" selected="True">Do not set</option>
66 <option value="megabytes">Set in megabytes</option>
67 <option value="gigabytes">Set in gigabytes</option>
68 </param>
69 <when value="default" >
70 <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/>
71 </when>
72 <when value="megabytes">
73 <param name="max_heap_size" type="integer" value="512" min="256" label="Maximum size, in megabytes, of the memory allocation pool" help="Examples: 256, 512, etc."/>
74 </when>
75 <when value="gigabytes">
76 <param name="max_heap_size" type="integer" value="1" min="1" label="Maximum size, in gigabytes, of the memory allocation pool" help="Examples: 1, 2, etc."/>
77 </when>
78 </conditional>
79 </xml>
80 <token name="@max_heap_size_args@">
81 --max_heap_size_type $set_max_heap_size.max_heap_size_type
82 --max_heap_size $set_max_heap_size.max_heap_size
83 </token>
84 <xml name="image_datatypes">
85 <option value="bmp">bmp</option>
86 <option value="gif">gif</option>
87 <option value="jpg">jpg</option>
88 <option value="png" selected="true">png</option>
89 <option value="tiff">tiff</option>
90 </xml>
91 <xml name="bunwarpj_citations">
92 <citations>
93 <citation type="bibtex">
94 @InProceedings(Arganda-Carreras2006,
95 author = "Ignacio Arganda-Carreras and
96 Carlos Oscar S{\'a}nchez Sorzano and
97 Roberto Marabini and
98 Jos{\'e} Mar\'{\i}a Carazo and
99 Carlos Ortiz-de-Solorzano and
100 Jan Kybic",
101 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",
102 publisher = "Springer Berlin / Heidelberg",
103 booktitle = "Computer Vision Approaches to Medical Image Analysis",
104 series = "Lecture Notes in Computer Science",
105 year = "2006",
106 volume = "4241",
107 pages = "85-95",
108 month = "May",
109 city = "Graz, Austria")
110 </citation>
111 <citation type="doi">10.1038/nmeth.2019</citation>
112 </citations>
113 </xml>
114 <xml name="fiji_headless_citations">
115 <citations>
116 <citation type="doi">10.1038/nmeth.2102</citation>
117 </citations>
118 </xml>
119 <xml name="bioformats_fiji_javabridge_citations">
120 <citations>
121 <citation type="doi">10.1038/nmeth.2102</citation>
122 <citation type="doi">10.1038/nmeth.2019</citation>
123 <citation type="doi">10.1083/jcb.201004104</citation>
124 </citations>
125 </xml>
126 </macros>