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comparison imagej2_analyze_skeleton.xml @ 2:9631aab7da53 draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:36:10 -0400
parents dd8e4e000d2f
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1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="1.0.0"> 2 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
3 <description>with ImageJ2</description> 3 <description>with ImageJ2</description>
4 <macros> 4 <macros>
5 <import>imagej2_macros.xml</import> 5 <import>imagej2_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="fiji_20141125_requirements" /> 7 <expand macro="fiji_requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 python $__tool_directory__/imagej2_analyze_skeleton.py 10 python $__tool_directory__/imagej2_analyze_skeleton.py
11 --input "$input" 11 --input "$input"
12 --input_datatype $input.ext 12 --input_datatype $input.ext
13 --black_background $black_background
13 --prune_cycle_method $prune_cycle_method 14 --prune_cycle_method $prune_cycle_method
14 --prune_ends $prune_ends 15 --prune_ends $prune_ends
15 --calculate_largest_shortest_path $calculate_largest_shortest_path 16 --calculate_largest_shortest_path $calculate_largest_shortest_path
16 --show_detailed_info $show_detailed_info 17 ##TODO: seel below--show_detailed_info $show_detailed_info
17 @max_heap_size_args@
18 --jython_script $__tool_directory__/jython_script.py 18 --jython_script $__tool_directory__/jython_script.py
19 --output "$output" 19 --output "$output"
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/> 23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
24 <expand macro="black_background_param" />
24 <param name="prune_cycle_method" type="select" label="Prune cycle method"> 25 <param name="prune_cycle_method" type="select" label="Prune cycle method">
25 <option value="none" selected="True">None</option> 26 <option value="none" selected="True">None</option>
26 <option value="shortest_branch">Shortest branch</option> 27 <option value="shortest_branch">Shortest branch</option>
27 <option value="lowest_intensity_voxel">Lowest intensity voxel</option> 28 <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
28 <option value="lowest_intensity_branch">Lowest intensity branch</option> 29 <option value="lowest_intensity_branch">Lowest intensity branch</option>
33 </param> 34 </param>
34 <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path"> 35 <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path">
35 <option value="no" selected="True">No</option> 36 <option value="no" selected="True">No</option>
36 <option value="yes">Yes</option> 37 <option value="yes">Yes</option>
37 </param> 38 </param>
39 <!-- TODO: Uncomment this option when the tool has been enhanced to use the
40 future "Display labeled skeletons" option. See http://fiji.sc/AnalyzeSkeleton.
38 <param name="show_detailed_info" type="select" label="Show detailed info"> 41 <param name="show_detailed_info" type="select" label="Show detailed info">
39 <option value="no" selected="True">No</option> 42 <option value="no" selected="True">No</option>
40 <option value="yes">Yes</option> 43 <option value="yes">Yes</option>
41 </param> 44 </param>
42 <expand macro="max_heap_size_type_conditional" /> 45 -->
43 </inputs> 46 </inputs>
44 <outputs> 47 <outputs>
45 <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> 48 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
46 </outputs> 49 </outputs>
47 <tests> 50 <tests>
61 <param name="input_datatype" value="gif" /> 64 <param name="input_datatype" value="gif" />
62 <param name="calculate_largest_shortest_path" value="yes" /> 65 <param name="calculate_largest_shortest_path" value="yes" />
63 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" /> 66 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
64 </test> 67 </test>
65 <test> 68 <test>
69 <!-- TODO: Change this test and the following test to set "show_detailed_info"
70 to "yes" when the tool has been enhanced to use the future "Display labeled skeletons"
71 option. See http://fiji.sc/AnalyzeSkeleton. -->
66 <param name="input" value="skeletonized_blobs.gif" /> 72 <param name="input" value="skeletonized_blobs.gif" />
67 <param name="input_datatype" value="gif" /> 73 <param name="input_datatype" value="gif" />
68 <param name="show_detailed_info" value="yes" /> 74 <!-- <param name="show_detailed_info" value="yes" /> -->
69 <output name="output" file="detailed.tabular" ftype="tabular" /> 75 <output name="output" file="detailed.tabular" ftype="tabular" />
70 </test> 76 </test>
71 <test> 77 <test>
72 <param name="input" value="skeletonized_clown.jpg" /> 78 <param name="input" value="skeletonized_clown.jpg" />
73 <param name="input_datatype" value="jpg" /> 79 <param name="input_datatype" value="jpg" />
74 <param name="prune_cycle_method" value="shortest_branch" /> 80 <param name="prune_cycle_method" value="shortest_branch" />
75 <param name="calculate_largest_shortest_path" value="yes" /> 81 <param name="calculate_largest_shortest_path" value="yes" />
76 <param name="show_detailed_info" value="yes" /> 82 <!-- <param name="show_detailed_info" value="yes" /> -->
77 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" /> 83 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
78 </test> 84 </test>
79 </tests> 85 </tests>
80 <help> 86 <help>
81 87
110 **Options** 116 **Options**
111 117
112 - **Prune cycle method**: prune the possible loops in the skeleton. 118 - **Prune cycle method**: prune the possible loops in the skeleton.
113 - **Prune ends**: prunes any branch that ends in an end-point. 119 - **Prune ends**: prunes any branch that ends in an end-point.
114 - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path). 120 - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
115 - **Show detailed info**: produces information about the branches of each skeleton in the image.
116 ]]> 121 ]]>
117 </help> 122 </help>
118 <citations> 123 <citations>
119 <citation type="doi">10.1002/jemt.20829</citation> 124 <citation type="doi">10.1002/jemt.20829</citation>
120 <citation type="doi">10.1038/nmeth.2102</citation> 125 <citation type="doi">10.1038/nmeth.2102</citation>