Mercurial > repos > imgteam > coordinates_of_roi
annotate coordinates_of_roi.xml @ 4:00175f4a2bbb draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
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date | Mon, 13 Nov 2023 22:10:52 +0000 |
parents | 02a686fc1654 |
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rev | line source |
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4
00175f4a2bbb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_coordinates_of_roi" name="Convert binary image to points (point coordinates)" version="0.0.4-2"> |
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0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description></description> |
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00175f4a2bbb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation> |
00175f4a2bbb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations> |
00175f4a2bbb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs> |
00175f4a2bbb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref> |
00175f4a2bbb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <requirements> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <requirement type="package" version="0.14.2">scikit-image</requirement> |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <requirement type="package" version="0.23.4">pandas</requirement> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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12 <requirement type="package" version="0.15.1">tifffile</requirement> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 </requirements> |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <command detect_errors="aggressive"> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <![CDATA[ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 python '$__tool_directory__/coordinates_of_roi.py' |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 '$im' |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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18 '$pixel_table' |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 $white_obj |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 --threshold $threshold |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 ]]> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 </command> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <inputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <param name="im" type="data" format="png" label="Source file" /> |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false" |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 label="Set to Yes if object is white and background black, otherwise set to No" /> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <param name="threshold" type="float" value="0.5" label="Threshold value" /> |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </inputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <outputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <data format="tabular" name="pixel_table" /> |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 </outputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <tests> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 <test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 <param name="im" value="test.png"/> |
0d30ffea8874
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <param name="white_obj" value="true"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit bfae746780819634a014388ea4671a49fc5c178d
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36 <output name="pixel_table" value="newtable.tsv" ftype="tabular"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 </test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 </tests> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <help> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 **What it does** |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI). |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 </help> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 <citations> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 </citations> |
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47 </tool> |