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comparison anisotropic_diffusion.xml @ 1:626be11c43fc draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
author thomaswollmann
date Wed, 12 Dec 2018 04:48:49 -0500
parents babb41158e9f
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0:babb41158e9f 1:626be11c43fc
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>