Mercurial > repos > imgteam > image_registration_affine

annotate image_registration_affine.xml @ 2:77dc68af2b40 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit ded1703bcd6e295b26201505edb58381991b265e"
author imgteam
date Mon, 28 Feb 2022 17:35:49 +0000
parents fa769715b6b0
children 5030651c2993
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77dc68af2b40 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit ded1703bcd6e295b26201505edb58381991b265e"
imgteam
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1 <tool id="ip_image_registration" name="Image Registration" version="0.0.3" profile="20.05">
0
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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2 <description>based on intensity information</description>
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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3 <requirements>
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4 <requirement type="package" version="0.18.1">scikit-image</requirement>
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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5 <requirement type="package" version="1.6.2">scipy</requirement>
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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6 <requirement type="package" version="1.2.4">pandas</requirement>
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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7 <requirement type="package" version="1.20.2">numpy</requirement>
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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8 <requirement type="package" version="2020.10.1">tifffile</requirement>
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9 </requirements>
1
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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10 <command detect_errors="aggressive">
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11 <![CDATA[
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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12 python '$__tool_directory__/image_registration_affine.py'
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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13 '$fn_moving'
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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14 '$fn_fixed'
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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15 '$fn_tmat'
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16 '$sigma'
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17 '$metric'
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18 ]]>
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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19 </command>
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20 <inputs>
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21 <param name="fn_moving" type="data" format="tiff,png,jpg" label="Moving image" />
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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22 <param name="fn_fixed" type="data" format="tiff,png,jpg" label="Fixed (reference) image" />
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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23 <param name="sigma" type="float" value="3" label="Sigma of Gaussian filter for smoothing input images" />
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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24 <param name="metric" type="select" label="Image similarity metric">
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25 <option value="mse" selected="True">Mean squared error</option>
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26 <option value="mae">Mean absolute error</option>
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27 <option value="lcc">Local cross-correlation</option>
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28 </param>
0
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" name="fn_tmat" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="fn_moving" value="moving.png"/>
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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36 <param name="fn_fixed" value="fixed.png"/>
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fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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37 <param name="sigma" value="3"/>
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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38 <param name="metric" value="lcc"/>
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39 <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
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40 </test>
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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41 </tests>
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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42 <help>
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43 **What it does**
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44
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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45 This tool estimates the (affine) transformation matrix for registration of two images based on intensity information.
e34222a620d4 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit 79c2fd560fce8ded4d7f7fe97e876871794e2f9d"
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46 </help>
1
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47 <citations>
fa769715b6b0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ commit e82400162e337b36c29d6e79fb2deb9871475397"
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48 </citations>
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49 </tool>