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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:12:09 +0000
parents 097b803aeb5d
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097b803aeb5d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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1 <tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with MedPy</description>
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3 <macros>
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4 <import>creators.xml</import>
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5 <import>tests.xml</import>
097b803aeb5d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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6 <token name="@TOOL_VERSION@">0.4.0</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
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8 </macros>
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9 <creator>
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10 <expand macro="creators/bmcv" />
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11 </creator>
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12 <edam_operations>
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13 <edam_operation>operation_3443</edam_operation>
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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14 </edam_operations>
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">medpy</requirement>
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17 <requirement type="package" version="1.20">numpy</requirement>
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18 <requirement type="package" version="0.18.1">scikit-image</requirement>
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19 <requirement type="package" version="0.1">giatools</requirement>
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20 </requirements>
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21 <command detect_errors="aggressive">
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22 <![CDATA[
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 python '$__tool_directory__/anisotropic_diffusion.py' '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption'
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 ]]>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="tiff" label="Input image"/>
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28 <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
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31 <param name="eqoption" type="select" label="Diffusion feature" help="Perona Malik diffusion equation">
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32 <option value="1" selected="True">Favor high contrast edges</option>
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33 <option value="2">Favor wide regions</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data format="tiff" name="output"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="galaxyIcon_noText.tif" />
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42 <param name="niter" value="100" />
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43 <param name="kappa" value="50" />
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44 <param name="gamma" value="0.1" />
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45 <param name="eqoption" value="1" />
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46 <expand macro="tests/intensity_image_diff" name="output" value="res.tif" ftype="tiff"/>
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47 </test>
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48 </tests>
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49 <help>
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50
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51 **Applies edge-preserving, anisotropic image diffusion.**
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52
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53 </help>
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54 <citations>
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55 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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56 </citations>
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57 </tool>