Mercurial > repos > imgteam > points_association_nn
view points_association_nn.xml @ 3:65210e69cf95 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit ae389b10be46633407effcc6856167f6e8bb2122"
author | imgteam |
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date | Sat, 09 Apr 2022 12:46:39 +0000 |
parents | b30aa285ac0a |
children | f3fad67af22c |
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<tool id="ip_points_association_nn" name="Association of points" version="0.0.3" profile="20.05"> <description>in consecutive frames (slices) using the nearest neighbor algorithm</description> <requirements> <requirement type="package" version="1.20.2">numpy</requirement> <requirement type="package" version="3.0.7">openpyxl</requirement> <requirement type="package" version="1.2.4">pandas</requirement> <requirement type="package" version="0.18.1">scikit-image</requirement> </requirements> <command> <![CDATA[ python '$__tool_directory__/points_association_nn.py' '$fn_in' ./output.xlsx '$nbpx' '$thres' '$minlen' ]]> </command> <inputs> <param name="fn_in" type="data" format="tabular" label="Coordinates (and intensities) of input points (tsv tabular)" /> <param name="nbpx" type="integer" value="6" optional="true" min="1" max="30" label="Neighborhood size (in pixel) for associating points" /> <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" /> <param name="minlen" type="float" value="50" optional="true" min="1.0" max="100.0" label="Minimum length of tracks (% of sequence length)" /> </inputs> <outputs> <data format="xlsx" name="fn_out" from_work_dir="output.xlsx" /> </outputs> <tests> <test> <param name="fn_in" value="spots_detected.tsv"/> <param name="nbpx" value="6"/> <param name="thres" value="25"/> <param name="minlen" value="50"/> <output name="fn_out" value="spots_linked.xlsx" ftype="xlsx" compare="sim_size"/> </test> </tests> <help> **What it does** This tool associates points in consecutive frames (slices) using the nearest neighbor algorithm. </help> <citations> <citation type="doi">10.1097/j.pain.0000000000002642</citation> </citations> </tool>