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comparison colorize_labels.xml @ 2:3aa2d054848a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:22 +0000
parents 43c80f3c3b60
children 2d1de6e7b113
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1:43c80f3c3b60 2:3aa2d054848a
1 <tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with NetworkX</description> 2 <description>with NetworkX</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
4 <token name="@TOOL_VERSION@">3.2.1</token> 6 <token name="@TOOL_VERSION@">3.2.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 8 </macros>
9 <creator>
10 <expand macro="creators/bmcv" />
11 </creator>
7 <edam_operations> 12 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 13 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 14 </edam_operations>
10 <requirements> 15 <requirements>
11 <requirement type="package" version="3.2.1">networkx</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
12 <requirement type="package" version="1.22">numpy</requirement> 17 <requirement type="package" version="1.22">numpy</requirement>
13 <requirement type="package" version="0.18.1">scikit-image</requirement> 18 <requirement type="package" version="0.18.1">scikit-image</requirement>
14 </requirements> 19 </requirements>
15 <command><![CDATA[ 20 <command><![CDATA[
16 21
40 <test> 45 <test>
41 <param name="input" value="input1.tif" /> 46 <param name="input" value="input1.tif" />
42 <param name="radius" value="1" /> 47 <param name="radius" value="1" />
43 <param name="bg_label" value="0" /> 48 <param name="bg_label" value="0" />
44 <param name="bg_color" value="#5a5a5a" /> 49 <param name="bg_color" value="#5a5a5a" />
45 <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1" /> 50 <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
51 <has_image_channels channels="3"/>
52 </expand>
46 </test> 53 </test>
47 <test> 54 <test>
48 <param name="input" value="input2.tif" /> 55 <param name="input" value="input2.tif" />
49 <param name="radius" value="10" /> 56 <param name="radius" value="10" />
50 <param name="bg_label" value="0" /> 57 <param name="bg_label" value="0" />
51 <param name="bg_color" value="#ffffff" /> 58 <param name="bg_color" value="#ffffff" />
52 <output name="output" value="output2.png" ftype="png" compare="sim_size" delta_frac="0.1" /> 59 <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
60 <has_image_channels channels="3"/>
61 </expand>
53 </test> 62 </test>
54 </tests> 63 </tests>
55 <help> 64 <help>
56 Colorize a 2-D label map for visualization using greedy coloring. 65
66 **Colorizes a 2-D label map for visualization using greedy coloring.**
57 67
58 Label maps are produced by segmentation and other image analysis steps. 68 Label maps are produced by segmentation and other image analysis steps.
59 Direct inspection of label maps can be difficult, 69 Direct inspection of label maps can be difficult,
60 because labels usually correspond to gray values which are difficult to 70 because labels usually correspond to gray values which are difficult to
61 distinguish visually from each other and from the image background. 71 distinguish visually from each other and from the image background.
62 To facilitate the visual inspection of label maps, this tools converts 72 To facilitate the visual inspection of label maps, this tools converts
63 label maps to color images, by assigning each label a unique color. 73 label maps to color images, by assigning each label a unique color.
74
64 </help> 75 </help>
65 <citations> 76 <citations>
66 <citation type="bibtex"> 77 <citation type="bibtex">
67 @inproceedings{networkx, 78 @inproceedings{networkx,
68 author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.}, 79 author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},