Mercurial > repos > imgteam > anisotropic_diffusion

annotate anisotropic_diffusion.xml @ 2:e6987afa0484 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:29 +0000
parents 17d3cfba9b5a
children 097b803aeb5d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
1 <tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="0.2-2">
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
2 <description>with MedPy</description>
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
3 <edam_operations>
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
4 <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
imgteam
parents: 1
diff changeset
5 </edam_operations>
0
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 <requirements>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
7 <requirement type="package" version="0.14.2">scikit-image</requirement>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
8 <requirement type="package" version="0.3.0">medpy</requirement>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9 <requirement type="package" version="1.15.4">numpy</requirement>
1
17d3cfba9b5a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
10 <requirement type="package" version="0.15.1">tifffile</requirement>
17d3cfba9b5a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
11 </requirements>
17d3cfba9b5a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
12 <command detect_errors="aggressive">
0
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13 <![CDATA[
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
14 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
imgteam
parents:
diff changeset
15 ]]>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
16 </command>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 <inputs>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
18 <param name="input" type="data" format="tiff" label="Image file"/>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 <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
imgteam
parents:
diff changeset
20 <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
imgteam
parents:
diff changeset
21 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
22 <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation">
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
23 <option value="1" selected="True">Favour high contrast edges</option>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
24 <option value="2">Favour wide regions</option>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
25 </param>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
26 </inputs>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
27 <outputs>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
28 <data format="tiff" name="output"/>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
29 </outputs>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
30 <tests>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
31 <test>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
32 <param name="input" value="galaxyIcon_noText.tif" />
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
33 <param name="niter" value="100" />
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
34 <param name="kappa" value="50" />
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
35 <param name="gamma" value="0.1" />
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
36 <param name="eqoption" value="1" />
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
37 <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
38 </test>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
39 </tests>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
40 <help>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
41 **What it does**
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
42
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
43 Edge-preserving, Anisotropic image diffusion
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
44 </help>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
45 <citations>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
46 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
47 </citations>
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
48 </tool>