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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
author imgteam
date Tue, 24 Sep 2024 17:30:11 +0000
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1 <tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with NetworkX</description>
3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">3.2.1</token>
7 <token name="@VERSION_SUFFIX@">3</token>
8 </macros>
9 <creator>
10 <expand macro="creators/bmcv" />
11 </creator>
12 <edam_operations>
13 <edam_operation>operation_3443</edam_operation>
14 </edam_operations>
15 <requirements>
16 <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
17 <requirement type="package" version="1.22">numpy</requirement>
18 <requirement type="package" version="0.18.1">scikit-image</requirement>
19 <requirement type="package" version="0.1">giatools</requirement>
20 </requirements>
21 <command><![CDATA[
22
23 ## Inputs
24
25 python '$__tool_directory__/colorize_labels.py' '$input'
26 --radius $radius
27 --bg_label $bg_label
28 --bg_color '$bg_color'
29
30 ## Outputs
31
32 --output output.png
33
34 ]]>
35 </command>
36 <inputs>
37 <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
38 <param argument="--radius" type="integer" min="1" value="10" label="Radius of the neighborhood" help="Defines the neighborhood (in pixels) where labels are considered to be adjacent." />
39 <param argument="--bg_label" type="integer" value="0" label="Background label" />
40 <param argument="--bg_color" type="color" value="#000000" label="Background color"/>
41 </inputs>
42 <outputs>
43 <data format="png" name="output" from_work_dir="output.png" />
44 </outputs>
45 <tests>
46 <!-- int64 -->
47 <test>
48 <param name="input" value="input1.tif" />
49 <param name="radius" value="1" />
50 <param name="bg_label" value="0" />
51 <param name="bg_color" value="#5a5a5a" />
52 <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
53 <has_image_channels channels="3"/>
54 </expand>
55 </test>
56 <!-- uint8 -->
57 <test>
58 <param name="input" value="input2.tif" />
59 <param name="radius" value="10" />
60 <param name="bg_label" value="0" />
61 <param name="bg_color" value="#ffffff" />
62 <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
63 <has_image_channels channels="3"/>
64 </expand>
65 </test>
66 <!-- uint16 -->
67 <test>
68 <param name="input" value="input3.tif" />
69 <param name="radius" value="100" />
70 <param name="bg_label" value="0" />
71 <param name="bg_color" value="#ffffff" />
72 <expand macro="tests/intensity_image_diff" name="output" value="output3.png" ftype="png">
73 <has_image_channels channels="3"/>
74 </expand>
75 </test>
76 </tests>
77 <help>
78
79 **Colorizes a 2-D label map for visualization using greedy coloring.**
80
81 Label maps are produced by segmentation and other image analysis steps.
82 Direct inspection of label maps can be difficult,
83 because labels usually correspond to gray values which are difficult to
84 distinguish visually from each other and from the image background.
85 To facilitate the visual inspection of label maps, this tools converts
86 label maps to color images, by assigning each label a unique color.
87
88 </help>
89 <citations>
90 <citation type="bibtex">
91 @inproceedings{networkx,
92 author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},
93 title = {Exploring network structure, dynamics, and function using {NetworkX}},
94 booktitle = {Proc. of the 7th Python in Science Conference (SciPy 2008)},
95 pages = {11--15},
96 year = {2008},
97 }
98 </citation>
99 </citations>
100 </tool>