Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
annotate 2d_filter_segmentation_by_features.xml @ 1:6ad1d3cfdea1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
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date | Mon, 13 Nov 2023 22:10:21 +0000 |
parents | e576b73a2e2f |
children | 8f76184ca03f |
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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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1 <tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-2"> |
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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2 <description></description> |
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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3 <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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4 <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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5 </edam_operations> |
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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6 <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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7 <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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8 </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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9 <requirements> |
0
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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10 <requirement type="package" version="0.14.2">scikit-image</requirement> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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11 <requirement type="package" version="5.3.0">pillow</requirement> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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12 <requirement type="package" version="0.23.4">pandas</requirement> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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13 <requirement type="package" version="0.15.1">tifffile</requirement> |
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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 </requirements> |
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 <command detect_errors="aggressive"> |
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 <![CDATA[ |
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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17 python '$__tool_directory__/2d_filter_segmentation_by_features.py' '$input' '$output' '$feature_file' '$rule_file' |
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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18 ]]> |
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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19 </command> |
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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20 <inputs> |
0
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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21 <param name="input" type="data" format="tiff" label="Source file" /> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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22 <param name="feature_file" type="data" format="tabular" label="Feature file" /> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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23 <param name="rule_file" type="data" format="tabular" label="Rules file" /> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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24 </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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25 <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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26 <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
imgteam
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27 </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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28 <tests> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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29 <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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30 <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
imgteam
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31 <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
imgteam
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32 <param name="rule_file" value="rules.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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33 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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34 </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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35 </tests> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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36 <help> |
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 Filter label image by rules (e.g., remove large or deformed objects). |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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38 Rules file has a specific format (cols: ,f1,2, rows: feature_name, min, max). The features have to be also profived in a specific format (cols: label, f1, f2). |
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 </help> |
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 <citations> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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41 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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42 </citations> |
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 </tool> |