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comparison landmark_registration.xml @ 3:9ccd642e7ae2 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
author imgteam
date Sat, 26 Feb 2022 17:14:05 +0000
parents 4e089a0983b1
children aee73493bf53
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2:4e089a0983b1 3:9ccd642e7ae2
1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.3" profile="20.05"> 1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.4" profile="20.05">
2 <description>estimates the affine transformation matrix</description> 2 <description>estimates the affine transformation matrix</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.18.1">scikit-image</requirement> 4 <requirement type="package" version="0.18.1">scikit-image</requirement>
5 <requirement type="package" version="1.6.2">scipy</requirement> 5 <requirement type="package" version="1.6.2">scipy</requirement>
6 <requirement type="package" version="1.2.4">pandas</requirement> 6 <requirement type="package" version="1.2.4">pandas</requirement>
10 <![CDATA[ 10 <![CDATA[
11 python '$__tool_directory__/landmark_registration.py' 11 python '$__tool_directory__/landmark_registration.py'
12 '$fn_pts1' 12 '$fn_pts1'
13 '$fn_pts2' 13 '$fn_pts2'
14 '$fn_tmat' 14 '$fn_tmat'
15 #if $algo_option.algo == 'ransac' 15 #if '$algo_option.algo' == 'ransac':
16 --res_th $algo_option.res_thr 16 --res_th $algo_option.res_thr
17 --max_ite $algo_option.max_iter 17 --max_ite $algo_option.max_iter
18 #end if 18 #end if
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <inputs>
21 <param name="fn_pts1" type="data" format="tabular" label="Coordinates of SRC landmarks (tsv file)" /> 21 <param name="fn_pts1" type="data" format="tabular" label="Coordinates of SRC landmarks (tsv file)" />
22 <param name="fn_pts2" type="data" format="tabular" label="Coordinates of DST landmarks (tsv file)" /> 22 <param name="fn_pts2" type="data" format="tabular" label="Coordinates of DST landmarks (tsv file)" />
37 </outputs> 37 </outputs>
38 <tests> 38 <tests>
39 <test> 39 <test>
40 <param name="fn_pts1" value="points_moving.tsv"/> 40 <param name="fn_pts1" value="points_moving.tsv"/>
41 <param name="fn_pts2" value="points_fixed.tsv"/> 41 <param name="fn_pts2" value="points_fixed.tsv"/>
42 <param name="algo_option.algo" value="ls"/> 42 <conditional name="algo_option">
43 <param name="algo" value="ls"/>
44 </conditional>
43 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/> 45 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
44 </test> 46 </test>
45 <test> 47 <test>
46 <param name="fn_pts1" value="points_moving.tsv"/> 48 <param name="fn_pts1" value="points_moving.tsv"/>
47 <param name="fn_pts2" value="points_fixed.tsv"/> 49 <param name="fn_pts2" value="points_fixed.tsv"/>
48 <param name="algo_option.algo" value="ransac"/> 50 <conditional name="algo_option">
49 <param name="algo_option.res_thr" value="2"/> 51 <param name="algo" value="ransac"/>
50 <param name="algo_option.max_iter" value="100"/> 52 <param name="res_thr" value="2"/>
53 <param name="max_iter" value="100"/>
54 </conditional>
51 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/> 55 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
52 </test> 56 </test>
53 </tests> 57 </tests>
54 <help> 58 <help>
55 **What it does** 59 **What it does**