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planemo upload commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author iuc
date Fri, 26 Jun 2015 05:29:22 -0400
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children 6beb1921064d
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <xml name="fiji_headless_requirements">
4 <requirements>
5 <requirement type="package" version="20141125">fiji</requirement>
6 </requirements>
7 </xml>
8 <xml name="python_bioformats_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="max_heap_size_type_conditional">
45 <conditional name="set_max_heap_size">
46 <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.">
47 <option value="default" selected="True">Do not set</option>
48 <option value="megabytes">Set in megabytes</option>
49 <option value="gigabytes">Set in gigabytes</option>
50 </param>
51 <when value="default">
52 <param name="max_heap_size" type="integer" value="0" label="Do not set" help="Use system default"/>
53 </when>
54 <when value="megabytes">
55 <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."/>
56 </when>
57 <when value="gigabytes">
58 <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."/>
59 </when>
60 </conditional>
61 </xml>
62 <token name="@max_heap_size_args@">
63 --max_heap_size_type $set_max_heap_size.max_heap_size_type
64 --max_heap_size $set_max_heap_size.max_heap_size
65 </token>
66 <xml name="image_datatypes">
67 <option value="bmp">bmp</option>
68 <option value="gif">gif</option>
69 <option value="jpg">jpg</option>
70 <option value="png" selected="true">png</option>
71 <option value="tiff">tiff</option>
72 </xml>
73 <xml name="bunwarpj_citations">
74 <citations>
75 <citation type="bibtex">
76 @InProceedings(Arganda-Carreras2006,
77 author = "Ignacio Arganda-Carreras and
78 Carlos Oscar S{\'a}nchez Sorzano and
79 Roberto Marabini and
80 Jos{\'e} Mar\'{\i}a Carazo and
81 Carlos Ortiz-de-Solorzano and
82 Jan Kybic",
83 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",
84 publisher = "Springer Berlin / Heidelberg",
85 booktitle = "Computer Vision Approaches to Medical Image Analysis",
86 series = "Lecture Notes in Computer Science",
87 year = "2006",
88 volume = "4241",
89 pages = "85-95",
90 month = "May",
91 city = "Graz, Austria")
92 </citation>
93 <citation type="doi">10.1038/nmeth.2019</citation>
94 </citations>
95 </xml>
96 <xml name="fiji_headless_citations">
97 <citations>
98 <citation type="doi">10.1038/nmeth.2102</citation>
99 </citations>
100 </xml>
101 <xml name="bioformats_fiji_javabridge_citations">
102 <citations>
103 <citation type="doi">10.1038/nmeth.2102</citation>
104 <citation type="doi">10.1038/nmeth.2019</citation>
105 <citation type="doi">10.1083/jcb.201004104</citation>
106 </citations>
107 </xml>
108 </macros>