Mercurial > repos > imgteam > image_registration_affine
comparison image_registration_affine.xml @ 1:fa769715b6b0 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
author | imgteam |
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date | Thu, 20 Jan 2022 00:45:30 +0000 |
parents | e34222a620d4 |
children | 77dc68af2b40 |
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0:e34222a620d4 | 1:fa769715b6b0 |
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1 <tool id="ip_image_registration" name="Image Registration" version="0.0.1"> | 1 <tool id="ip_image_registration" name="Image Registration" version="0.0.2" profile="20.05"> |
2 <description>based on intensity information</description> | 2 <description>based on intensity information</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.14.2">scikit-image</requirement> | 4 <requirement type="package" version="0.18.1">scikit-image</requirement> |
5 <requirement type="package" version="1.1.0">scipy</requirement> | 5 <requirement type="package" version="1.6.2">scipy</requirement> |
6 <requirement type="package" version="0.23.4">pandas</requirement> | 6 <requirement type="package" version="1.2.4">pandas</requirement> |
7 <requirement type="package" version="1.15.2">numpy</requirement> | 7 <requirement type="package" version="1.20.2">numpy</requirement> |
8 <requirement type="package" version="0.15.1">tifffile</requirement> | 8 <requirement type="package" version="2020.10.1">tifffile</requirement> |
9 </requirements> | 9 </requirements> |
10 <command> | 10 <command detect_errors="aggressive"> |
11 <![CDATA[ | 11 <![CDATA[ |
12 python '$__tool_directory__/image_registration_affine.py' | 12 python '$__tool_directory__/image_registration_affine.py' |
13 '$fn_moving' | 13 '$fn_moving' |
14 '$fn_fixed' | 14 '$fn_fixed' |
15 '$fn_tmat' | 15 '$fn_tmat' |
16 '$sigma' | |
17 '$metric' | |
16 ]]> | 18 ]]> |
17 </command> | 19 </command> |
18 <inputs> | 20 <inputs> |
19 <param name="fn_moving" type="data" format="png" label="Moving Image" /> | 21 <param name="fn_moving" type="data" format="tiff,png,jpg" label="Moving image" /> |
20 <param name="fn_fixed" type="data" format="png" label="Fixed Image" /> | 22 <param name="fn_fixed" type="data" format="tiff,png,jpg" label="Fixed (reference) image" /> |
23 <param name="sigma" type="float" value="3" label="Sigma of Gaussian filter for smoothing input images" /> | |
24 <param name="metric" type="select" label="Image similarity metric"> | |
25 <option value="lcc" selected="True">Local cross-correlation</option> | |
26 <option value="mse">Mean squared error</option> | |
27 <option value="mae">Mean absolute error</option> | |
28 </param> | |
21 </inputs> | 29 </inputs> |
22 <outputs> | 30 <outputs> |
23 <data format="tabular" name="fn_tmat" /> | 31 <data format="tabular" name="fn_tmat" /> |
24 </outputs> | 32 </outputs> |
25 <tests> | 33 <tests> |
26 <test> | 34 <test> |
27 <param name="fn_moving" value="moving.png"/> | 35 <param name="fn_moving" value="moving.png"/> |
28 <param name="fn_fixed" value="fixed.png"/> | 36 <param name="fn_fixed" value="fixed.png"/> |
37 <param name="sigma" value="3"/> | |
38 <param name="metric" value="lcc"/> | |
29 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/> | 39 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/> |
30 </test> | 40 </test> |
31 </tests> | 41 </tests> |
32 <help> | 42 <help> |
33 **What it does** | 43 **What it does** |
34 | 44 |
35 This tool estimates the (affine) transformation matrix for registration of two images based on intensity information. | 45 This tool estimates the (affine) transformation matrix for registration of two images based on intensity information. |
36 </help> | 46 </help> |
47 <citations> | |
48 </citations> | |
37 </tool> | 49 </tool> |