Mercurial > repos > thomaswollmann > anisotropic_diffusion
comparison anisotropic_diffusion.xml @ 1:6be26440a8ec draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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date | Wed, 16 Jan 2019 15:33:19 -0500 |
parents | 9a30c8f0f651 |
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0:9a30c8f0f651 | 1:6be26440a8ec |
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1 <tool id="anisotropic_diffusion" name="Anisotropic Diffusion" version="0.1"> | 1 <tool id="anisotropic_diffusion" name="Anisotropic Diffusion" version="0.1"> |
2 <description>Edge-preserving, Anisotropic diffusion</description> | 2 <description>Edge-preserving, Anisotropic diffusion</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.12.3" >scikit-image</requirement> | 4 <requirement type="package" version="0.14.0" >scikit-image</requirement> |
5 <requirement type="package" version="0.2.2">medpy</requirement> | 5 <requirement type="package" version="0.3.0">medpy</requirement> |
6 <requirement type="package" version="1.12">numpy</requirement> | 6 <requirement type="package" version="1.15.4">numpy</requirement> |
7 </requirements> | 7 </requirements> |
8 <command> | 8 <command> |
9 <![CDATA[ | 9 <![CDATA[ |
10 python "$__tool_directory__/anisotropic_diffusion.py" '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption' | 10 python "$__tool_directory__/anisotropic_diffusion.py" '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption' |
11 ]]> | 11 ]]> |
12 </command> | 12 </command> |
13 <inputs> | 13 <inputs> |
14 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file"/> | 14 <param name="input" type="data" format="tiff" label="Image file"/> |
15 <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/> | 15 <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/> |
16 <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/> | 16 <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/> |
17 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/> | 17 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/> |
18 <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation"> | 18 <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation"> |
19 <option value="1" selected="True">Favour high contrast edges</option> | 19 <option value="1" selected="True">Favour high contrast edges</option> |
23 <outputs> | 23 <outputs> |
24 <data format="tiff" name="output"/> | 24 <data format="tiff" name="output"/> |
25 </outputs> | 25 </outputs> |
26 <tests> | 26 <tests> |
27 <test> | 27 <test> |
28 <param name="input" value="galaxyIcon_noText.png" /> | 28 <param name="input" value="galaxyIcon_noText.tif" /> |
29 <param name="niter" value="100" /> | 29 <param name="niter" value="100" /> |
30 <param name="kappa" value="50" /> | 30 <param name="kappa" value="50" /> |
31 <param name="gamma" value="0.1" /> | 31 <param name="gamma" value="0.1" /> |
32 <param name="eqoption" value="1" /> | 32 <param name="eqoption" value="1" /> |
33 <output name="output" ftype="tiff" /> | 33 <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/> |
34 </test> | 34 </test> |
35 </tests> | 35 </tests> |
36 <help>Edge-preserving, Anisotropic image diffusion.</help> | 36 <help>Edge-preserving, Anisotropic image diffusion.</help> |
37 <citations> | 37 <citations> |
38 <citation type="doi">10.1109/34.56205</citation> | 38 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
39 </citations> | 39 </citations> |
40 </tool> | 40 </tool> |