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annotate landmark_registration.xml @ 6:02aa2873e67d draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:23 +0000
parents 12997d4c5b00
children
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6
02aa2873e67d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_landmark_registration" name="Perform affine image registration (landmark-based)" version="0.1.0-2" profile="20.05">
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2 <description></description>
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3 <edam_operations>
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4 <edam_operation>operation_3443</edam_operation>
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5 </edam_operations>
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6 <xrefs>
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
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8 </xrefs>
0
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9 <requirements>
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10 <requirement type="package" version="0.18.1">scikit-image</requirement>
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11 <requirement type="package" version="1.6.2">scipy</requirement>
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12 <requirement type="package" version="1.2.4">pandas</requirement>
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13 <requirement type="package" version="1.20.2">numpy</requirement>
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14 </requirements>
2
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15 <command detect_errors="aggressive">
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16 <![CDATA[
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17 python '$__tool_directory__/landmark_registration.py'
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18 '$fn_lmkmov'
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19 '$fn_lmkfix'
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20 '$fn_out'
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21 #if $algo_option.algo == "pwat"
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22 --pwlt '$algo_option.fn_ptsmov'
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23 #elif $algo_option.algo == "ransac"
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24 --res_th $algo_option.res_th
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25 --max_ite $algo_option.max_ite
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26 #end if
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param name="fn_lmkmov" type="data" format="tabular" label="Coordinates of moving landmarks (tsv file)" />
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31 <param name="fn_lmkfix" type="data" format="tabular" label="Coordinates of fixed landmarks (tsv file)" />
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32 <conditional name="algo_option">
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33 <param name="algo" type="select" label="Select the algorithm">
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34 <option value="ransac">Affine Transformation (based on RANSAC)</option>
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35 <option value="ls">Affine Transformation (based on Least Squares)</option>
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36 <option value="pwat" selected="True">Piecewise Affine Transformation</option>
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37 </param>
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38 <when value="ransac">
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39 <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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40 <param name="max_ite" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
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41 </when>
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42 <when value="ls"></when>
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43 <when value="pwat">
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44 <param name="fn_ptsmov" type="data" format="tabular" label="Coordinates of points to be transformed (tsv file)" />
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45 </when>
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46 </conditional>
0
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47 </inputs>
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48 <outputs>
4
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49 <data format="tabular" name="fn_out" />
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50 </outputs>
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51 <tests>
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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="ls"/>
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56 <output name="fn_out" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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57 </test>
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58 <test>
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59 <param name="fn_lmkmov" value="points_moving.tsv"/>
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60 <param name="fn_lmkfix" value="points_fixed.tsv"/>
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61 <param name="algo" value="ransac"/>
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62 <param name="res_th" value="2.0"/>
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63 <param name="max_ite" value="100"/>
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64 <output name="fn_out" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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65 </test>
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66 <test>
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67 <param name="fn_lmkmov" value="lmk_mov.tsv"/>
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68 <param name="fn_lmkfix" value="lmk_fix.tsv"/>
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69 <param name="algo" value="pwat"/>
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70 <param name="fn_ptsmov" value="points.tsv"/>
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71 <output name="fn_out" value="points_pwlt.tsv" ftype="tabular"/>
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72 </test>
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73 </tests>
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74 <help>
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75 **What it does**
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76
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77 1) Estimation of the affine transformation matrix between two sets of 2d points;
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78 2) Piecewise affine transformation of points based on landmark pairs.
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79
4
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80 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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81 </help>
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82 <citations>
5
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83 <citation type="doi">10.3390/cells11152390</citation>
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84 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
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85 </citations>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
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86 </tool>