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comparison superdsm.xml @ 0:1b0fc671187f draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
author imgteam
date Sun, 25 Jun 2023 21:48:40 +0000
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1 <tool id="ip_superdsm" name="SuperDSM" version="0.1.2-1" profile="20.05">
2 <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
3 <requirements>
4 <requirement type="package" version="0.1.2">superdsm</requirement>
5 <requirement type="package" version="1.6.0">ray-core</requirement>
6 <requirement type="package" version="0.18.1">scikit-image</requirement>
7 </requirements>
8 <command detect_errors="aggressive">
9 <![CDATA[
10 python '$__tool_directory__/run-superdsm.py'
11 '${dataset}'
12 'cfg.json'
13 'masks.png'
14 'overlay.png'
15 $seg_border
16 \${GALAXY_SLOTS:-4}
17 > stdout.txt
18 ]]>
19 </command>
20 <inputs>
21 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
22 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" />
23 <!--
24 <section name="config" title="Hyperparameters" expanded="false">
25 </section>
26 -->
27 </inputs>
28 <outputs>
29 <data format="txt" name="stdout" from_work_dir="stdout.txt" label="${tool.name} on ${on_string}: stdout" />
30 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" />
31 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" />
32 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" />
33 </outputs>
34 <tests>
35 <test>
36 <param name="dataset" value="BBBC033_C2_z28.png" />
37 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
38 </test>
39 </tests>
40 <help>
41 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
42
43 You can either use an individual input image (PNG, TIF) or a collection of such images.
44 </help>
45 <citations>
46 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
47 </citations>
48 </tool>