Mercurial > repos > imgteam > image_registration_affine

comparison image_registration_affine.xml @ 1:fa769715b6b0 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
author imgteam
date Thu, 20 Jan 2022 00:45:30 +0000
parents e34222a620d4
children 77dc68af2b40
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0:e34222a620d4 1:fa769715b6b0
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>