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comparison imagej2_macros.xml @ 3:bb65623b90a8 draft

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planemo upload commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
author iuc
date Tue, 04 Aug 2015 11:15:10 -0400
parents ea7a01d0f218
children 48f25b8408e1
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2:ea7a01d0f218 3:bb65623b90a8
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros> 2 <macros>
3 <xml name="fiji_headless_requirements"> 3 <xml name="fiji_20141125_requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="20141125">fiji</requirement> 5 <requirement type="package" version="20141125">fiji</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <xml name="python_bioformats_requirements"> 8 <xml name="python_bioformats_104_requirements">
9 <requirements> 9 <requirements>
10 <requirement type="package" version="20141125">fiji</requirement> 10 <requirement type="package" version="20141125">fiji</requirement>
11 <requirement type="package" version="1.0.11">javabridge</requirement> 11 <requirement type="package" version="1.0.11">javabridge</requirement>
12 <requirement type="package" version="1.9">numpy</requirement> 12 <requirement type="package" version="1.9">numpy</requirement>
13 <requirement type="package" version="1.0.4">python_bioformats</requirement> 13 <requirement type="package" version="1.0.4">python_bioformats</requirement>
39 <option value="RGB_black">RGB black</option> 39 <option value="RGB_black">RGB black</option>
40 <option value="RGB_random">RGB random</option> 40 <option value="RGB_random">RGB random</option>
41 <option value="RGB_ramp">RGB ramp</option> 41 <option value="RGB_ramp">RGB ramp</option>
42 </param> 42 </param>
43 </xml> 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>
44 <xml name="max_heap_size_type_conditional"> 62 <xml name="max_heap_size_type_conditional">
45 <conditional name="set_max_heap_size"> 63 <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."> 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.">
47 <option value="default" selected="True">Do not set</option> 65 <option value="default" selected="True">Do not set</option>
48 <option value="megabytes">Set in megabytes</option> 66 <option value="megabytes">Set in megabytes</option>
49 <option value="gigabytes">Set in gigabytes</option> 67 <option value="gigabytes">Set in gigabytes</option>
50 </param> 68 </param>
51 <when value="default"> 69 <when value="default" >
52 <param name="max_heap_size" type="integer" value="0" label="Do not set" help="Use system default"/> 70 <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/>
53 </when> 71 </when>
54 <when value="megabytes"> 72 <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."/> 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."/>
56 </when> 74 </when>
57 <when value="gigabytes"> 75 <when value="gigabytes">