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annotate points_association_nn.xml @ 1:d6655b83dc13 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit ef82d0882741042922349499cafa35d20d70ce70"
author imgteam
date Thu, 22 Jul 2021 22:29:43 +0000
parents a16e6ada200e
children e291ea59cb38
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a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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1 <tool id="ip_points_association_nn" name="Association of points" version="0.0.1" profile="20.05">
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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2 <description>in consecutive frames (slices) using the nearest neighbor algorithm</description>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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3 <requirements>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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4 <requirement type="package" version="1.20.2">numpy</requirement>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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5 <requirement type="package" version="3.0.7">openpyxl</requirement>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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6 <requirement type="package" version="1.2.4">pandas</requirement>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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7 <requirement type="package" version="0.18.1">scikit-image</requirement>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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8 </requirements>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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9 <command>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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10 <![CDATA[
1
d6655b83dc13 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit ef82d0882741042922349499cafa35d20d70ce70"
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11 python '$__tool_directory__/points_association_nn.py'
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a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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12 '$fn_in'
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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13 ./output.xlsx
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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14 '$nbpx'
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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15 '$thres'
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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16 '$minlen'
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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17 ]]>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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18 </command>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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19 <inputs>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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20 <param name="fn_in" type="data" format="tabular" label="Name of input file (tsv tabular)" />
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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21 <param name="nbpx" type="integer" value="6" label="Neighborhood size in pixel" />
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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22 <param name="thres" type="float" value="25" label="Percentage (%) of the global maximal intensity for thresholding some event" />
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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23 <param name="minlen" type="float" value="50" label="Minimum length of tracks (% of sequence length)" />
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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24 </inputs>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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25 <outputs>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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26 <data format="xlsx" name="fn_out" from_work_dir="output.xlsx" />
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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27 </outputs>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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28 <tests>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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29 <test>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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30 <param name="fn_in" value="spots_detected.tsv"/>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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31 <param name="nbpx" value="6"/>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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32 <param name="thres" value="25"/>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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33 <param name="minlen" value="50"/>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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34 <output name="fn_out" value="spots_linked.xlsx" ftype="xlsx" compare="sim_size"/>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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35 </test>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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36 </tests>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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37 <help>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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38 **What it does**
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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39
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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40 This tool associates points in consecutive frames (slices) using the nearest neighbor algorithm.
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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41 </help>
a16e6ada200e "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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42 </tool>