Mercurial > repos > imgteam > colorize_labels
comparison colorize_labels.xml @ 1:43c80f3c3b60 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
author | imgteam |
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date | Wed, 13 Mar 2024 19:08:34 +0000 |
parents | 0afb17e107ff |
children | 3aa2d054848a |
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0:0afb17e107ff | 1:43c80f3c3b60 |
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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 SuperDSM</description> | 2 <description>with NetworkX</description> |
3 <macros> | 3 <macros> |
4 <token name="@TOOL_VERSION@">0.2.0</token> | 4 <token name="@TOOL_VERSION@">3.2.1</token> |
5 <token name="@VERSION_SUFFIX@">0</token> | 5 <token name="@VERSION_SUFFIX@">0</token> |
6 </macros> | 6 </macros> |
7 <edam_operations> | 7 <edam_operations> |
8 <edam_operation>operation_3443</edam_operation> | 8 <edam_operation>operation_3443</edam_operation> |
9 </edam_operations> | 9 </edam_operations> |
10 <xrefs> | |
11 <xref type="bio.tools">superdsm</xref> | |
12 <xref type="biii">superdsm</xref> | |
13 </xrefs> | |
14 <requirements> | 10 <requirements> |
15 <requirement type="package" version="0.2.0">superdsm</requirement> | 11 <requirement type="package" version="3.2.1">networkx</requirement> |
16 <requirement type="package" version="1.20">numpy</requirement> | 12 <requirement type="package" version="1.22">numpy</requirement> |
17 <requirement type="package" version="0.18.1">scikit-image</requirement> | 13 <requirement type="package" version="0.18.1">scikit-image</requirement> |
18 </requirements> | 14 </requirements> |
19 <command><![CDATA[ | 15 <command><![CDATA[ |
20 | 16 |
21 ## Inputs | 17 ## Inputs |
22 | 18 |
23 python '$__tool_directory__/colorize_labels.py' '$input' | 19 python '$__tool_directory__/colorize_labels.py' '$input' |
24 --seed $seed | 20 --radius $radius |
25 --bg_label $bg_label | 21 --bg_label $bg_label |
26 --bg_color '$bg_color' | 22 --bg_color '$bg_color' |
27 | 23 |
28 ## Outputs | 24 ## Outputs |
29 | 25 |
31 | 27 |
32 ]]> | 28 ]]> |
33 </command> | 29 </command> |
34 <inputs> | 30 <inputs> |
35 <param name="input" type="data" format="tiff,png" label="Input image (label map)" /> | 31 <param name="input" type="data" format="tiff,png" label="Input image (label map)" /> |
36 <param argument="--seed" type="integer" value="0" label="Randomization seed" /> | 32 <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." /> |
37 <param argument="--bg_label" type="integer" value="0" label="Background label" /> | 33 <param argument="--bg_label" type="integer" value="0" label="Background label" /> |
38 <param argument="--bg_color" type="color" value="#000000" label="Background color"/> | 34 <param argument="--bg_color" type="color" value="#000000" label="Background color"/> |
39 </inputs> | 35 </inputs> |
40 <outputs> | 36 <outputs> |
41 <data format="png" name="output" from_work_dir="output.png" /> | 37 <data format="png" name="output" from_work_dir="output.png" /> |
42 </outputs> | 38 </outputs> |
43 <tests> | 39 <tests> |
44 <test> | 40 <test> |
45 <param name="input" value="input1.tif"/> | 41 <param name="input" value="input1.tif" /> |
46 <param name="bg_label" value="0"/> | 42 <param name="radius" value="1" /> |
47 <param name="bg_color" value="#5a5a5a"/> | 43 <param name="bg_label" value="0" /> |
48 <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1"/> | 44 <param name="bg_color" value="#5a5a5a" /> |
45 <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1" /> | |
46 </test> | |
47 <test> | |
48 <param name="input" value="input2.tif" /> | |
49 <param name="radius" value="10" /> | |
50 <param name="bg_label" value="0" /> | |
51 <param name="bg_color" value="#ffffff" /> | |
52 <output name="output" value="output2.png" ftype="png" compare="sim_size" delta_frac="0.1" /> | |
49 </test> | 53 </test> |
50 </tests> | 54 </tests> |
51 <help> | 55 <help> |
52 Colorize a 2-D label map for visualization. | 56 Colorize a 2-D label map for visualization using greedy coloring. |
53 | 57 |
54 Label maps are produced by segmentation and other image analysis steps. | 58 Label maps are produced by segmentation and other image analysis steps. |
55 Direct inspection of label maps can be difficult, | 59 Direct inspection of label maps can be difficult, |
56 because labels usually correspond to gray values which are difficult to | 60 because labels usually correspond to gray values which are difficult to |
57 distinguish visually from each other and from the image background. | 61 distinguish visually from each other and from the image background. |
58 To facilitate the visual inspection of label maps, this tools converts | 62 To facilitate the visual inspection of label maps, this tools converts |
59 label maps to color images, by assigning each label a unique color. | 63 label maps to color images, by assigning each label a unique color. |
60 </help> | 64 </help> |
61 <citations> | 65 <citations> |
62 <citation type="doi">10.1109/TPAMI.2022.3185583</citation> | 66 <citation type="bibtex"> |
67 @inproceedings{networkx, | |
68 author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.}, | |
69 title = {Exploring network structure, dynamics, and function using {NetworkX}}, | |
70 booktitle = {Proc. of the 7th Python in Science Conference (SciPy 2008)}, | |
71 pages = {11--15}, | |
72 year = {2008}, | |
73 } | |
74 </citation> | |
63 </citations> | 75 </citations> |
64 </tool> | 76 </tool> |