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annotate landmark_registration.xml @ 5:12997d4c5b00 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit 6d6a6fd04fa1d1f9a5bf1aff451e43be072c0293
author imgteam
date Wed, 03 Aug 2022 16:50:52 +0000
parents aee73493bf53
children 02aa2873e67d
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1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.1.0" profile="20.05">
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2 <description>estimates the affine transformation matrix or performs piecewise affine transformation</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_lmkmov'
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13 '$fn_lmkfix'
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14 '$fn_out'
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15 #if $algo_option.algo == "pwat"
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16 --pwlt '$algo_option.fn_ptsmov'
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17 #elif $algo_option.algo == "ransac"
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18 --res_th $algo_option.res_th
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19 --max_ite $algo_option.max_ite
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20 #end if
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="fn_lmkmov" type="data" format="tabular" label="Coordinates of moving landmarks (tsv file)" />
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25 <param name="fn_lmkfix" type="data" format="tabular" label="Coordinates of fixed landmarks (tsv file)" />
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26 <conditional name="algo_option">
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27 <param name="algo" type="select" label="Select the algorithm">
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28 <option value="ransac">Affine Transformation (based on RANSAC)</option>
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29 <option value="ls">Affine Transformation (based on Least Squares)</option>
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30 <option value="pwat" selected="True">Piecewise Affine Transformation</option>
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31 </param>
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32 <when value="ransac">
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33 <param name="res_th" type="float" value="2.0" label="Maximum distance for a data point to be classified as an inlier." />
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34 <param name="max_ite" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
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35 </when>
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36 <when value="ls"></when>
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37 <when value="pwat">
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38 <param name="fn_ptsmov" type="data" format="tabular" label="Coordinates of points to be transformed (tsv file)" />
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39 </when>
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40 </conditional>
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41 </inputs>
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42 <outputs>
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43 <data format="tabular" name="fn_out" />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="fn_lmkmov" value="points_moving.tsv"/>
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48 <param name="fn_lmkfix" value="points_fixed.tsv"/>
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49 <param name="algo" value="ls"/>
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50 <output name="fn_out" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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51 </test>
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52 <test>
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53 <param name="fn_lmkmov" value="points_moving.tsv"/>
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54 <param name="fn_lmkfix" value="points_fixed.tsv"/>
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55 <param name="algo" value="ransac"/>
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56 <param name="res_th" value="2.0"/>
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57 <param name="max_ite" value="100"/>
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58 <output name="fn_out" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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59 </test>
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60 <test>
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61 <param name="fn_lmkmov" value="lmk_mov.tsv"/>
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62 <param name="fn_lmkfix" value="lmk_fix.tsv"/>
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63 <param name="algo" value="pwat"/>
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64 <param name="fn_ptsmov" value="points.tsv"/>
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65 <output name="fn_out" value="points_pwlt.tsv" ftype="tabular"/>
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66 </test>
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67 </tests>
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68 <help>
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69 **What it does**
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70
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71 1) Estimation of the affine transformation matrix between two sets of 2d points;
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72 2) Piecewise affine transformation of points based on landmark pairs.
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73
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74 About the format of landmark/point coordinates in the input TSV table: Columns with header "x" and "y" are for x- and y-coordinate, respectively.
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75 </help>
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76 <citations>
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77 <citation type="doi">10.3390/cells11152390</citation>
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78 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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79 </citations>
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80 </tool>