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comparison colorize_labels.xml @ 0:0afb17e107ff draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
author imgteam
date Tue, 12 Mar 2024 23:00:45 +0000
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children 43c80f3c3b60
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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 SuperDSM</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <edam_operations>
8 <edam_operation>operation_3443</edam_operation>
9 </edam_operations>
10 <xrefs>
11 <xref type="bio.tools">superdsm</xref>
12 <xref type="biii">superdsm</xref>
13 </xrefs>
14 <requirements>
15 <requirement type="package" version="0.2.0">superdsm</requirement>
16 <requirement type="package" version="1.20">numpy</requirement>
17 <requirement type="package" version="0.18.1">scikit-image</requirement>
18 </requirements>
19 <command><![CDATA[
20
21 ## Inputs
22
23 python '$__tool_directory__/colorize_labels.py' '$input'
24 --seed $seed
25 --bg_label $bg_label
26 --bg_color '$bg_color'
27
28 ## Outputs
29
30 --output output.png
31
32 ]]>
33 </command>
34 <inputs>
35 <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
36 <param argument="--seed" type="integer" value="0" label="Randomization seed" />
37 <param argument="--bg_label" type="integer" value="0" label="Background label" />
38 <param argument="--bg_color" type="color" value="#000000" label="Background color"/>
39 </inputs>
40 <outputs>
41 <data format="png" name="output" from_work_dir="output.png" />
42 </outputs>
43 <tests>
44 <test>
45 <param name="input" value="input1.tif"/>
46 <param name="bg_label" value="0"/>
47 <param name="bg_color" value="#5a5a5a"/>
48 <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
49 </test>
50 </tests>
51 <help>
52 Colorize a 2-D label map for visualization.
53
54 Label maps are produced by segmentation and other image analysis steps.
55 Direct inspection of label maps can be difficult,
56 because labels usually correspond to gray values which are difficult to
57 distinguish visually from each other and from the image background.
58 To facilitate the visual inspection of label maps, this tools converts
59 label maps to color images, by assigning each label a unique color.
60 </help>
61 <citations>
62 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
63 </citations>
64 </tool>