Mercurial > repos > iuc > biapy
annotate macros.xml @ 0:e434d9b9cd13 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
| author | iuc |
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| date | Thu, 09 Oct 2025 07:42:36 +0000 |
| parents | |
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| rev | line source |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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changeset
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1 <macros> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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2 <token name="@TOOL_VERSION@">3.6.5</token> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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3 <token name="@VERSION_SUFFIX@">0</token> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
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4 <token name="@PROFILE@">25.0</token> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
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5 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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6 <xml name="requirements"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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7 <requirements> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
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8 <requirement type="package" version="3.10.18">python</requirement> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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9 <requirement type="package" version="@TOOL_VERSION@">biapy</requirement> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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10 <requirement type="package" version="4.10.0">opencv</requirement> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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11 <requirement type="package" version="3.3.3">openexr</requirement> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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12 <requirement type="package" version="0.5.3">safetensors</requirement> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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13 </requirements> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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14 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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15 <xml name="creators"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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16 <creator> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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17 <person givenName="Daniel" familyName="Franco" url="https://danifranco.github.io/" identifier="https://orcid.org/0000-0002-1109-110X" /> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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18 </creator> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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19 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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20 <xml name="citations"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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21 <citations> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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22 <citation type="doi">10.1038/s41592-025-02699-y</citation> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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23 <yield/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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24 </citations> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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25 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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26 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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27 <!-- Q9 --> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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28 <xml name="train_raw_param"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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29 <param name="raw_train" type="data" format="tiff,tif,png,jpg,h5" multiple="true" label="Specify the training raw images" help="Select the training images; all must have the same number of channels, and each channel should contain the same type of information (see https://biapy.readthedocs.io/en/latest/get_started/how_it_works.html for details)."/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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30 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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31 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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32 <xml name="train_raw_param_opt"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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33 <param name="raw_train" type="data" optional="true" format="tiff,tif,png,jpg,h5" multiple="true" label="Specify the training raw images" help="Select the training images; all must have the same number of channels, and each channel should contain the same type of information (see https://biapy.readthedocs.io/en/latest/get_started/how_it_works.html for details)."/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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34 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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35 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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36 <!-- Q10 --> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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37 <xml name="train_gt_param"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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38 <param name="gt_train" type="data" format="tiff,tif,png,jpg,h5,csv,txt" multiple="true" label="Specify the training ground truth (target) images" help="Select the ground truth (target) data for training; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image); see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details."/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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39 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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40 <xml name="train_gt_param_opt"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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41 <param name="gt_train" type="data" optional="true" format="tiff,tif,png,jpg,h5,csv,txt" multiple="true" label="Specify the training ground truth (target) images" help="Select the ground truth (target) data for training; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image); see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details."/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
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42 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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43 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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44 <!-- Q11 --> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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45 <xml name="test_raw_param"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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46 <param name="raw_test" type="data" format="tiff,tif,png,jpg,h5" multiple="true" label="Specify the test raw images" help="Select the test images; all must have the same number of channels, and each channel should contain the same type of information to avoid confusing the model."/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
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47 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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48 <xml name="test_raw_param_opt"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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49 <param name="raw_test" type="data" format="tiff,tif,png,jpg,h5" optional="true" multiple="true" label="Specify the test raw images" help="Select the test images; all must have the same number of channels, and each channel should contain the same type of information to avoid confusing the model."/> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
diff
changeset
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50 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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51 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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52 <!-- Q13: REQUIRED test GT --> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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53 <xml name="test_gt_param_required"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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54 <param name="gt_test" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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55 type="data" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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56 format="tiff,tif,png,jpg,h5,csv,txt" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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57 multiple="true" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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58 label="Specify the test ground truth/target images" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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59 help="Select the ground truth (target) data for testing; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image); see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details." |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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60 optional="false" /> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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61 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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62 |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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63 <!-- Q13: OPTIONAL test GT --> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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64 <xml name="test_gt_param_optional"> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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65 <param name="gt_test" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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66 type="data" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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67 format="tiff,tif,png,jpg,h5,csv,txt" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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68 multiple="true" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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69 label="Specify the test ground truth/target images (optional)" |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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70 help="Select the ground truth (target) data for testing; the expected format depends on the workflow (e.g. masks for semantic/instance segmentation, centroid files for detection, high-res images for super-resolution, paired images for image-to-image). If provided, BiaPy will compute workflow-specific evaluation metrics on the test set. See https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for details." |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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71 optional="true" /> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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72 </xml> |
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e434d9b9cd13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents:
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73 </macros> |