Mercurial > repos > imgteam > points_association_nn
comparison points_association_nn.xml @ 0:04e692ee53a8 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
| author | imgteam |
|---|---|
| date | Thu, 22 Jul 2021 22:29:47 +0000 |
| parents | |
| children | fd4293bee0dc |
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| -1:000000000000 | 0:04e692ee53a8 |
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| 1 <tool id="ip_points_association_nn" name="Association of points" version="0.0.1" profile="20.05"> | |
| 2 <description>in consecutive frames (slices) using the nearest neighbor algorithm</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.20.2">numpy</requirement> | |
| 5 <requirement type="package" version="3.0.7">openpyxl</requirement> | |
| 6 <requirement type="package" version="1.2.4">pandas</requirement> | |
| 7 <requirement type="package" version="0.18.1">scikit-image</requirement> | |
| 8 </requirements> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 python '$__tool_directory__/points_association_nn.py' | |
| 12 '$fn_in' | |
| 13 ./output.xlsx | |
| 14 '$nbpx' | |
| 15 '$thres' | |
| 16 '$minlen' | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param name="fn_in" type="data" format="tabular" label="Name of input file (tsv tabular)" /> | |
| 21 <param name="nbpx" type="integer" value="6" label="Neighborhood size in pixel" /> | |
| 22 <param name="thres" type="float" value="25" label="Percentage (%) of the global maximal intensity for thresholding some event" /> | |
| 23 <param name="minlen" type="float" value="50" label="Minimum length of tracks (% of sequence length)" /> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="xlsx" name="fn_out" from_work_dir="output.xlsx" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="fn_in" value="spots_detected.tsv"/> | |
| 31 <param name="nbpx" value="6"/> | |
| 32 <param name="thres" value="25"/> | |
| 33 <param name="minlen" value="50"/> | |
| 34 <output name="fn_out" value="spots_linked.xlsx" ftype="xlsx" compare="sim_size"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 **What it does** | |
| 39 | |
| 40 This tool associates points in consecutive frames (slices) using the nearest neighbor algorithm. | |
| 41 </help> | |
| 42 </tool> |