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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
author imgteam
date Tue, 06 Jan 2026 09:25:17 +0000
parents 5530132d500e
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5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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1 <macros>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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2
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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3 <!-- Macros for validation of inputs -->
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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4
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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5 <xml name="validators/is_single_channel">
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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6 <!--
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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7 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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8 hence not inherit the metadata fields like `channels`. To cope with that, we allow all datasets
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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9 except those where we *know* that they are *not* single-channel.
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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10 -->
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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11 <validator type="expression" message="Dataset is a multi-channel image"
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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12 ><![CDATA[getattr(value.metadata, "channels", None) in (None, '') or int(value.metadata.channels) < 2]]></validator>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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13 </xml>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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14
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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15 <xml name="validators/is_single_frame">
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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16 <!--
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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17 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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18 hence not inherit the metadata fields like `frames`. To cope with that, we allow all datasets
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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19 except those where we *know* that they are *not* single-frame.
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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20 -->
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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21 <validator type="expression" message="Dataset is a multi-frame image"
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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22 ><![CDATA[getattr(value.metadata, "frames", None) in (None, '') or int(value.metadata.frames) < 2]]></validator>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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23 </xml>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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24
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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25 <xml name="validators/is_2d">
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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26 <!--
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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27 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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28 hence not inherit the metadata fields like `depth`. To cope with that, we allow all datasets
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
imgteam
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29 except those where we *know* that they are *not* 2-D.
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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30 -->
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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31 <validator type="expression" message="Dataset is a 3-D image"
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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32 ><![CDATA[getattr(value.metadata, "depth", None) in (None, '') or int(value.metadata.depth) < 2]]></validator>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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33 </xml>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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34
7
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
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35 <xml name="validators/is_3d">
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
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36 <!--
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
parents: 5
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37 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
parents: 5
diff changeset
38 hence not inherit the metadata fields like `depth`. To cope with that, we allow all datasets
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
parents: 5
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39 except those where we *know* that they are *not* 3-D.
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
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40 -->
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
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41 <validator type="expression" message="Dataset is a 2-D image"
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
imgteam
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42 ><![CDATA[getattr(value.metadata, "depth", None) in (None, '') or int(value.metadata.depth) >= 2]]></validator>
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
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parents: 5
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43 </xml>
048545339ced planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
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44
5
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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45 <xml name="validators/is_binary">
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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46 <!--
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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47 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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48 hence not inherit the metadata fields like `num_unique_values`. To cope with that, we allow all
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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49 datasets except those where we *know* that they are *not* binary.
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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50 -->
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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51 <validator type="expression" message="Dataset is not a binary image"
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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52 ><![CDATA[getattr(value.metadata, "num_unique_values", None) in (None, '') or int(value.metadata.num_unique_values) <= 2]]></validator>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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53 </xml>
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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54
5530132d500e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
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55 </macros>