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comparison anisotropic_diffusion.xml @ 3:097b803aeb5d draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:48 +0000
parents e6987afa0484
children 6ad5de2c5b7c
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2:e6987afa0484 3:097b803aeb5d
1 <tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="0.2-2"> 1 <tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with MedPy</description> 2 <description>with MedPy</description>
3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">0.4.0</token>
7 <token name="@VERSION_SUFFIX@">0</token>
8 </macros>
9 <creator>
10 <expand macro="creators/bmcv" />
11 </creator>
3 <edam_operations> 12 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 13 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 14 </edam_operations>
6 <requirements> 15 <requirements>
7 <requirement type="package" version="0.14.2">scikit-image</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">medpy</requirement>
8 <requirement type="package" version="0.3.0">medpy</requirement> 17 <requirement type="package" version="1.20">numpy</requirement>
9 <requirement type="package" version="1.15.4">numpy</requirement> 18 <requirement type="package" version="0.18.1">scikit-image</requirement>
10 <requirement type="package" version="0.15.1">tifffile</requirement>
11 </requirements> 19 </requirements>
12 <command detect_errors="aggressive"> 20 <command detect_errors="aggressive">
13 <![CDATA[ 21 <![CDATA[
14 python '$__tool_directory__/anisotropic_diffusion.py' '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption' 22 python '$__tool_directory__/anisotropic_diffusion.py' '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption'
15 ]]> 23 ]]>
16 </command> 24 </command>
17 <inputs> 25 <inputs>
18 <param name="input" type="data" format="tiff" label="Image file"/> 26 <param name="input" type="data" format="tiff" label="Input image"/>
19 <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/> 27 <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/>
20 <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/> 28 <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/>
21 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/> 29 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
22 <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation"> 30 <param name="eqoption" type="select" label="Diffusion feature" help="Perona Malik diffusion equation">
23 <option value="1" selected="True">Favour high contrast edges</option> 31 <option value="1" selected="True">Favor high contrast edges</option>
24 <option value="2">Favour wide regions</option> 32 <option value="2">Favor wide regions</option>
25 </param> 33 </param>
26 </inputs> 34 </inputs>
27 <outputs> 35 <outputs>
28 <data format="tiff" name="output"/> 36 <data format="tiff" name="output"/>
29 </outputs> 37 </outputs>
32 <param name="input" value="galaxyIcon_noText.tif" /> 40 <param name="input" value="galaxyIcon_noText.tif" />
33 <param name="niter" value="100" /> 41 <param name="niter" value="100" />
34 <param name="kappa" value="50" /> 42 <param name="kappa" value="50" />
35 <param name="gamma" value="0.1" /> 43 <param name="gamma" value="0.1" />
36 <param name="eqoption" value="1" /> 44 <param name="eqoption" value="1" />
37 <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/> 45 <expand macro="tests/intensity_image_diff" name="output" value="res.tif" ftype="tiff"/>
38 </test> 46 </test>
39 </tests> 47 </tests>
40 <help> 48 <help>
41 **What it does**
42 49
43 Edge-preserving, Anisotropic image diffusion 50 **Applies edge-preserving, anisotropic image diffusion.**
51
44 </help> 52 </help>
45 <citations> 53 <citations>
46 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 54 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
47 </citations> 55 </citations>
48 </tool> 56 </tool>