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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 04:54:43 -0400
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1 <tool id="ip_2d_split_binaryimage_by_watershed" name="Split objects" version="0.0.1">
2 <description>Split binary image by using watershed</description>
3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="1.15.4">numpy</requirement>
6 <requirement type="package" version="5.3.0">pillow</requirement>
7 <requirement type="package" version="0.15.1">tifffile</requirement>
8 <requirement type="package" version="1.2.1">scipy</requirement>
9 </requirements>
10 <command detect_errors="aggressive">
11 <![CDATA[
12 python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
13 ]]>
14 </command>
15 <inputs>
16 <param name="input" type="data" format="tiff" label="Source file" />
17 <param name="min_distance" type="integer" value="5" label="Minimum distance between two objects." />
18 </inputs>
19 <outputs>
20 <data format="tiff" name="output" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="input" value="in.tif"/>
25 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
26 <param name="min_distance" value="10"/>
27 </test>
28 </tests>
29 <help>
30 Split binary image by using distance transform and watershed.
31 </help>
32 <citations>
33 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
34 </citations>
35 </tool>