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annotate validators.xml @ 4:8f0dd9a58ec3 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
author imgteam
date Sat, 03 Jan 2026 14:14:05 +0000
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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1 <macros>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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3 <!-- Macros for validation of inputs -->
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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5 <xml name="validators/is_single_channel">
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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6 <!--
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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7 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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8 hence not inherit the metadata fields like `channels`. To cope with that, we allow all datasets
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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9 except those where we *know* that they are *not* single-channel.
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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10 -->
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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11 <validator type="expression" message="Dataset is a multi-channel image"
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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12 ><![CDATA[getattr(value.metadata, "channels", None) in (None, '') or int(value.metadata.channels) < 2]]></validator>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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13 </xml>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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15 <xml name="validators/is_single_frame">
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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16 <!--
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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17 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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18 hence not inherit the metadata fields like `frames`. To cope with that, we allow all datasets
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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19 except those where we *know* that they are *not* single-frame.
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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20 -->
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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21 <validator type="expression" message="Dataset is a multi-frame image"
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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22 ><![CDATA[getattr(value.metadata, "frames", None) in (None, '') or int(value.metadata.frames) < 2]]></validator>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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23 </xml>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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25 <xml name="validators/is_2d">
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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26 <!--
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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27 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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28 hence not inherit the metadata fields like `depth`. To cope with that, we allow all datasets
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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29 except those where we *know* that they are *not* 2-D.
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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30 -->
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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31 <validator type="expression" message="Dataset is a 3-D image"
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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32 ><![CDATA[getattr(value.metadata, "depth", None) in (None, '') or int(value.metadata.depth) < 2]]></validator>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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33 </xml>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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35 <xml name="validators/is_binary">
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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36 <!--
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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37 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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38 hence not inherit the metadata fields like `num_unique_values`. To cope with that, we allow all
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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39 datasets except those where we *know* that they are *not* binary.
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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40 -->
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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41 <validator type="expression" message="Dataset is not a binary image"
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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42 ><![CDATA[getattr(value.metadata, "num_unique_values", None) in (None, '') or int(value.metadata.num_unique_values) <= 2]]></validator>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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43 </xml>
8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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8f0dd9a58ec3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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45 </macros>