Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
annotate 2d_filter_segmentation_by_features.xml @ 3:9d47aabda459 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author | imgteam |
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date | Wed, 24 Apr 2024 08:11:47 +0000 |
parents | 8f76184ca03f |
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9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
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1 <tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-4" profile="20.05"> |
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8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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2 <description></description> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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3 <macros> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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4 <import>creators.xml</import> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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5 <import>tests.xml</import> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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6 </macros> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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7 <creator> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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8 <expand macro="creators/bmcv" /> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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9 </creator> |
1
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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10 <edam_operations> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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11 <edam_operation>operation_3443</edam_operation> |
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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12 </edam_operations> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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13 <xrefs> |
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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14 <xref type="bio.tools">galaxy_image_analysis</xref> |
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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15 </xrefs> |
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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16 <requirements> |
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9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
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17 <requirement type="package" version="0.18.1">scikit-image</requirement> |
9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
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18 <requirement type="package" version="2.2.2">pandas</requirement> |
9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
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19 <requirement type="package" version="2020.10.1">tifffile</requirement> |
9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
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20 <requirement type="package" version="0.1">giatools</requirement> |
1
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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21 </requirements> |
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8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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22 <command detect_errors="aggressive"><![CDATA[ |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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23 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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24 python '$__tool_directory__/2d_filter_segmentation_by_features.py' |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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25 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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26 '$input' |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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27 '$output' |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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28 '$feature_file' |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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29 '$rule_file' |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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30 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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31 ]]></command> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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32 <inputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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33 <param name="input" type="data" format="tiff" label="Label map" /> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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34 <param name="feature_file" type="data" format="tabular" label="Features" /> |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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35 <param name="rule_file" type="data" format="tabular" label="Rules" /> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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36 </inputs> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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37 <outputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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38 <data format="tiff" name="output" /> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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39 </outputs> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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40 <tests> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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41 <test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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42 <param name="input" value="in.tif"/> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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43 <param name="feature_file" value="features.tabular"/> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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44 <param name="rule_file" value="rules.tabular"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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45 <expand macro="tests/label_image_diff" name="output" value="out.tif" ftype="tiff"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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46 </test> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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47 </tests> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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48 <help> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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49 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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50 **Filters a label map by rules (e.g., remove large or deformed objects).** |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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51 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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52 The properties of the labeled image regions (features) must be provided in a specific tabular format |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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53 (columns: ``label``, ``feature1``, ``feature2``, and so on, where ``feature1`` and ``feature2`` can be arbitrary strings). |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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54 Each row corresponds to a labeled image region. |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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55 An example is given below. |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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56 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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57 +-------+-------+---------------------+ |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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58 | label | area | eccentricity | |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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59 +-------+-------+---------------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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60 | 1 | 344 | 0.42521053699241596 | |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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61 +-------+-------+---------------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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62 | 2 | 434 | 0.47679001553231926 | |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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63 +-------+-------+---------------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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64 | 3 | 907 | 0.9973539531125177 | |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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65 +-------+-------+---------------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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66 | 4 | 14320 | 0.17131009631035327 | |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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67 +-------+-------+---------------------+ |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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68 |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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69 The rules also must be supplied in a specific tabular format with three rows. |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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70 The top-left cell is empty, and the rest of the first row corresponds to the feature names (such as ``feature1`` or ``feature2``, see above). |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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71 The rest of the first column corresponds to the two values ``min`` and ``max``. |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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72 Each of the rows defines the minimum and maximum values for the corresponding features. |
8f76184ca03f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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73 A labeled image region is retrained if and only if it passes all checks with repsect to the given ``min`` and ``max`` values. |
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74 An example is given below. |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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75 |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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76 +-----+--------+--------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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77 | | area | eccentricity | |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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78 +-----+--------+--------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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79 | min | 500 | 0. | |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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80 +-----+--------+--------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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81 | max | 100000 | 0.5 | |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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82 +-----+--------+--------------+ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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83 |
0
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84 </help> |
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85 <citations> |
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86 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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87 </citations> |
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88 </tool> |