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comparison landmark_registration.xml @ 2:4e089a0983b1 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit 927b78d47c31714776ccdf3d16f26c3779298abb"
author imgteam
date Sun, 20 Feb 2022 15:46:58 +0000
parents a71239f3543a
children 9ccd642e7ae2
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1:b0503eec7bd6 2:4e089a0983b1
1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.2"> 1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.3" profile="20.05">
2 <description>Landmark Registration</description> 2 <description>estimates the affine transformation matrix</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="0.23.4">pandas</requirement> 5 <requirement type="package" version="1.6.2">scipy</requirement>
6 <requirement type="package" version="1.15.4">numpy</requirement> 6 <requirement type="package" version="1.2.4">pandas</requirement>
7 <requirement type="package" version="1.20.2">numpy</requirement>
7 </requirements> 8 </requirements>
8 <command><![CDATA[ 9 <command detect_errors="aggressive">
9 python '$__tool_directory__/landmark_registration.py' 10 <![CDATA[
10 --residual_threshold $residual_threshold 11 python '$__tool_directory__/landmark_registration.py'
11 --max_trials $max_trials 12 '$fn_pts1'
12 '$points_file1' 13 '$fn_pts2'
13 '$points_file2' 14 '$fn_tmat'
14 '$warp_matrix' 15 #if $algo_option.algo == 'ransac'
16 --res_th $algo_option.res_thr
17 --max_ite $algo_option.max_iter
18 #end if
15 ]]></command> 19 ]]></command>
16 <inputs> 20 <inputs>
17 <param name="points_file1" type="data" format="tabular" label="Path to tab-separated file with src points" /> 21 <param name="fn_pts1" type="data" format="tabular" label="Coordinates of SRC landmarks (tsv file)" />
18 <param name="points_file2" type="data" format="tabular" label="Path to tab-separated file with dst points" /> 22 <param name="fn_pts2" type="data" format="tabular" label="Coordinates of DST landmarks (tsv file)" />
19 <param name="residual_threshold" type="float" value="2" label="Maximum distance for a data point to be classified as an inlier." /> 23 <conditional name="algo_option">
20 <param name="max_trials" type="integer" value="100" label="Maximum number of iterations for random sample selection." /> 24 <param name="algo" type="select" label="Select the algorithm">
25 <option value="ransac" selected="True">RANSAC</option>
26 <option value="ls">Least Squares</option>
27 </param>
28 <when value="ransac">
29 <param name="res_thr" type="float" value="2.0" label="Maximum distance for a data point to be classified as an inlier." />
30 <param name="max_iter" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
31 </when>
32 <when value="ls"></when>
33 </conditional>
21 </inputs> 34 </inputs>
22 <outputs> 35 <outputs>
23 <data format="tabular" name="warp_matrix" /> 36 <data format="tabular" name="fn_tmat" />
24 </outputs> 37 </outputs>
25 <tests> 38 <tests>
26 <test> 39 <test>
27 <param name="points_file1" value="points1.tsv"/> 40 <param name="fn_pts1" value="points_moving.tsv"/>
28 <param name="points_file2" value="points2.tsv"/> 41 <param name="fn_pts2" value="points_fixed.tsv"/>
29 <param name="residual_threshold" value="2"/> 42 <param name="algo_option.algo" value="ls"/>
30 <param name="max_trials" value="100"/> 43 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
31 <output name="warp_matrix" value="warp.tsv" ftype="tabular" compare="diff" lines_diff="6"/> 44 </test>
45 <test>
46 <param name="fn_pts1" value="points_moving.tsv"/>
47 <param name="fn_pts2" value="points_fixed.tsv"/>
48 <param name="algo_option.algo" value="ransac"/>
49 <param name="algo_option.res_thr" value="2"/>
50 <param name="algo_option.max_iter" value="100"/>
51 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
32 </test> 52 </test>
33 </tests> 53 </tests>
34 <help> 54 <help>
35 **What it does** 55 **What it does**
36 56
37 This tool estimates the transformation matrix between two sets of 2d points. 57 This tool estimates the transformation matrix between two sets of 2d points.
58
59 About the format of landmark coordinates in the input TSV table: Columns with header "x" and "y" are for x- and y-coordinate, respectively.
38 </help> 60 </help>
39 <citations> 61 <citations>
40 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 62 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
41 </citations> 63 </citations>
42 </tool> 64 </tool>