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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 17:00:45 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
3 <description></description>
4 <macros>
5 <import>imagej2_macros.xml</import>
6 </macros>
7 <expand macro="fiji_requirements" />
8 <command>
9 <![CDATA[
10 python $__tool_directory__/imagej2_analyze_skeleton.py
11 --input "$input"
12 --input_datatype $input.ext
13 --black_background $black_background
14 --prune_cycle_method $prune_cycle_method
15 --prune_ends $prune_ends
16 --calculate_largest_shortest_path $calculate_largest_shortest_path
17 ##TODO: seel below--show_detailed_info $show_detailed_info
18 --jython_script $__tool_directory__/imagej2_analyze_skeleton_jython_script.py
19 --output "$output"
20 ]]>
21 </command>
22 <inputs>
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" />
25 <param name="prune_cycle_method" type="select" label="Prune cycle method">
26 <option value="none" selected="True">None</option>
27 <option value="shortest_branch">Shortest branch</option>
28 <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
29 <option value="lowest_intensity_branch">Lowest intensity branch</option>
30 </param>
31 <param name="prune_ends" type="select" label="Prune ends">
32 <option value="no" selected="True">No</option>
33 <option value="yes">Yes</option>
34 </param>
35 <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path">
36 <option value="no" selected="True">No</option>
37 <option value="yes">Yes</option>
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.
41 <param name="show_detailed_info" type="select" label="Show detailed info">
42 <option value="no" selected="True">No</option>
43 <option value="yes">Yes</option>
44 </param>
45 -->
46 </inputs>
47 <outputs>
48 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
49 </outputs>
50 <tests>
51 <test>
52 <param name="input" value="skeletonized_blobs.gif" />
53 <param name="input_datatype" value="gif" />
54 <output name="output" file="basic.tabular" ftype="tabular" />
55 </test>
56 <test>
57 <param name="input" value="skeletonized_clown.jpg" />
58 <param name="input_datatype" value="jpg" />
59 <param name="prune_cycle_method" value="shortest_branch" />
60 <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
61 </test>
62 <test>
63 <param name="input" value="skeletonized_blobs.gif" />
64 <param name="input_datatype" value="gif" />
65 <param name="calculate_largest_shortest_path" value="yes" />
66 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
67 </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. -->
72 <param name="input" value="skeletonized_blobs.gif" />
73 <param name="input_datatype" value="gif" />
74 <!-- <param name="show_detailed_info" value="yes" /> -->
75 <output name="output" file="detailed.tabular" ftype="tabular" />
76 </test>
77 <test>
78 <param name="input" value="skeletonized_clown.jpg" />
79 <param name="input_datatype" value="jpg" />
80 <param name="prune_cycle_method" value="shortest_branch" />
81 <param name="calculate_largest_shortest_path" value="yes" />
82 <!-- <param name="show_detailed_info" value="yes" /> -->
83 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
84 </test>
85 </tests>
86 <help>
87
88 .. class:: warningmark
89
90 The underlying AnalyzeSkeleton Fiji plugin works on binary images, so other image types will
91 automatically be converted to binary before they are analyzed. This step is performed using the
92 ImageJ2 **Make Binary** command with the following settings: **Iterations:** 1, **Count:** 1,
93 **Black background:** No, **Pad edges when eroding:** No. If these settings are not appropriate,
94 first manually convert the image to binary using the **Convert to binary (black and white) with
95 ImageJ2** tool, which allows you to change them.
96
97 .. class:: warningmark
98
99 The **Skeletonize images** tool produces skeleton images that can be used as input to this tool.
100 Images that have not been skeletonized will not result in errors, but the results may or may not
101 be useful.
102
103 **What it does**
104
105 <![CDATA[
106 Tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple
107 points and branches, and measures their average and maximum length. The voxels are classified into
108 three different categories depending on their 26 neighbors:
109
110 - **End-point** voxels: if they have less than 2 neighbors.
111 - **Junction** voxels: if they have more than 2 neighbors.
112 - **Slab** voxels: if they have exactly 2 neighbors.
113
114 -----
115
116 **Options**
117
118 - **Prune cycle method**: prune the possible loops in the skeleton.
119 - **Prune ends**: prunes any branch that ends in an end-point.
120 - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
121 ]]>
122 </help>
123 <citations>
124 <citation type="doi">10.1002/jemt.20829</citation>
125 <citation type="doi">10.1038/nmeth.2102</citation>
126 </citations>
127 </tool>