Mercurial > repos > imgteam > label_to_binary

comparison label_to_binary.xml @ 0:5da15c3bafed draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ commit 0a64a49d4a0ac3438544244a8b871be2fc144766
author imgteam
date Wed, 13 Mar 2024 14:55:31 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5da15c3bafed
1 <tool id="label_to_binary" name="Convert label map to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2 <description>with NumPy</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.26.4</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">galaxy_image_analysis</xref>
12 </xrefs>
13 <requirements>
14 <requirement type="package" version="1.26.4">numpy</requirement>
15 <requirement type="package" version="0.18.1">scikit-image</requirement>
16 </requirements>
17 <command><![CDATA[
18
19 ## Inputs
20
21 python '$__tool_directory__/label_to_binary.py'
22 '$input'
23 '$bg_label'
24
25 ## Outputs
26
27 ./output.tif
28
29 ]]>
30 </command>
31 <inputs>
32 <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
33 <param argument="--bg_label" type="integer" value="0" label="Background label" />
34 </inputs>
35 <outputs>
36 <data format="tiff" name="output" from_work_dir="output.tif" />
37 </outputs>
38 <tests>
39 <test>
40 <param name="input" value="input1.tif" />
41 <param name="bg_label" value="0" />
42 <output name="output" value="output1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
43 </test>
44 </tests>
45 <help>
46 This tools converts a label map (objects labeled by different labels/values) to a binary image.
47
48 The input image is converted by assigning white (pixel value 255) to image regions corresponding to labeled objects,
49 and black (pixel value 0) to image regions corresponding to image background (by default, this is label 0).
50 </help>
51 <citations>
52 <citation type="doi">10.1038/s41586-020-2649-2</citation>
53 </citations>
54 </tool>