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annotate 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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1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.4" profile="20.05">
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2 <description>estimates the affine transformation matrix</description>
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3 <requirements>
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4 <requirement type="package" version="0.18.1">scikit-image</requirement>
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5 <requirement type="package" version="1.6.2">scipy</requirement>
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6 <requirement type="package" version="1.2.4">pandas</requirement>
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7 <requirement type="package" version="1.20.2">numpy</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 python '$__tool_directory__/landmark_registration.py'
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12 '$fn_pts1'
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13 '$fn_pts2'
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14 '$fn_tmat'
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15 #if '$algo_option.algo' == 'ransac':
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16 --res_th $algo_option.res_thr
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17 --max_ite $algo_option.max_iter
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18 #end if
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19 ]]></command>
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20 <inputs>
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21 <param name="fn_pts1" type="data" format="tabular" label="Coordinates of SRC landmarks (tsv file)" />
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22 <param name="fn_pts2" type="data" format="tabular" label="Coordinates of DST landmarks (tsv file)" />
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23 <conditional name="algo_option">
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24 <param name="algo" type="select" label="Select the algorithm">
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25 <option value="ransac" selected="True">RANSAC</option>
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26 <option value="ls">Least Squares</option>
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27 </param>
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28 <when value="ransac">
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29 <param name="res_thr" type="float" value="2.0" label="Maximum distance for a data point to be classified as an inlier." />
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30 <param name="max_iter" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
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31 </when>
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32 <when value="ls"></when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
2
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36 <data format="tabular" name="fn_tmat" />
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37 </outputs>
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38 <tests>
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39 <test>
2
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40 <param name="fn_pts1" value="points_moving.tsv"/>
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41 <param name="fn_pts2" value="points_fixed.tsv"/>
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42 <conditional name="algo_option">
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43 <param name="algo" value="ls"/>
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44 </conditional>
2
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45 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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46 </test>
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47 <test>
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48 <param name="fn_pts1" value="points_moving.tsv"/>
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49 <param name="fn_pts2" value="points_fixed.tsv"/>
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50 <conditional name="algo_option">
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51 <param name="algo" value="ransac"/>
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52 <param name="res_thr" value="2"/>
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53 <param name="max_iter" value="100"/>
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54 </conditional>
2
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55 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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56 </test>
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57 </tests>
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58 <help>
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59 **What it does**
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60
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
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61 This tool estimates the transformation matrix between two sets of 2d points.
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62
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63 About the format of landmark coordinates in the input TSV table: Columns with header "x" and "y" are for x- and y-coordinate, respectively.
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64 </help>
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65 <citations>
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66 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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67 </citations>
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68 </tool>