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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:50 +0000
parents 65210e69cf95
children
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f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_points_association_nn" name="Perform linking in time series (nearest neighbors)" version="0.0.3-2" profile="20.05">
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations>
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation>
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations>
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
f3fad67af22c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
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9 <requirements>
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10 <requirement type="package" version="1.20.2">numpy</requirement>
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11 <requirement type="package" version="3.0.7">openpyxl</requirement>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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12 <requirement type="package" version="1.2.4">pandas</requirement>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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13 <requirement type="package" version="0.18.1">scikit-image</requirement>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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14 </requirements>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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15 <command>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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16 <![CDATA[
2
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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17 python '$__tool_directory__/points_association_nn.py'
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18 '$fn_in'
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19 ./output.xlsx
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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20 '$nbpx'
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21 '$thres'
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22 '$minlen'
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23 ]]>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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24 </command>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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25 <inputs>
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26 <param name="fn_in" type="data" format="tabular" label="Coordinates (and intensities) of input points (tsv tabular)" />
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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27 <param name="nbpx" type="integer" value="6" optional="true" min="1" max="30" label="Neighborhood size (in pixel) for associating points" />
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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28 <param name="thres" type="float" value="25" optional="true" min="0.0" max="99.9" label="Tracks with all intensities lower than certain percentage (%) of the global maximal intensity will be discarded" />
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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29 <param name="minlen" type="float" value="50" optional="true" min="1.0" max="100.0" label="Minimum length of tracks (% of sequence length)" />
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30 </inputs>
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31 <outputs>
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32 <data format="xlsx" name="fn_out" from_work_dir="output.xlsx" />
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33 </outputs>
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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34 <tests>
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35 <test>
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36 <param name="fn_in" value="spots_detected.tsv"/>
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37 <param name="nbpx" value="6"/>
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38 <param name="thres" value="25"/>
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39 <param name="minlen" value="50"/>
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40 <output name="fn_out" value="spots_linked.xlsx" ftype="xlsx" compare="sim_size"/>
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41 </test>
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42 </tests>
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43 <help>
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44 **What it does**
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45
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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46 This tool associates points in consecutive frames (slices) using the nearest neighbor algorithm.
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47 </help>
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48 <citations>
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49 <citation type="doi">10.1097/j.pain.0000000000002642</citation>
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50 </citations>
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51 </tool>