Mercurial > repos > bgruening > bioimage_inference
comparison bioimage_inference.xml @ 4:2b61d8fcfa52 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging commit f038722c21eaa3018e1cef0004ac7bd283d15269
| author | bgruening |
|---|---|
| date | Mon, 07 Apr 2025 14:46:13 +0000 |
| parents | bc28236f407b |
| children | 37b9ead209da |
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| 3:bc28236f407b | 4:2b61d8fcfa52 |
|---|---|
| 1 <tool id="bioimage_inference" name="Process image using a BioImage.IO model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> | 1 <tool id="bioimage_inference" name="Process image using a BioImage.IO model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> |
| 2 <description>with PyTorch</description> | 2 <description>with PyTorch</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@TOOL_VERSION@">2.4.1</token> | 4 <token name="@TOOL_VERSION@">2.4.1</token> |
| 5 <token name="@VERSION_SUFFIX@">1</token> | 5 <token name="@VERSION_SUFFIX@">2</token> |
| 6 </macros> | 6 </macros> |
| 7 <creator> | 7 <creator> |
| 8 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> | 8 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> |
| 9 <person givenName="Anup" familyName="Kumar" email="kumara@informatik.uni-freiburg.de" /> | 9 <person givenName="Anup" familyName="Kumar" email="kumara@informatik.uni-freiburg.de" /> |
| 10 <person givenName="Beatriz" familyName="Serrano-Solano" email="beatriz.serrano.solano@eurobioimaging.eu" /> | 10 <person givenName="Beatriz" familyName="Serrano-Solano" email="beatriz.serrano.solano@eurobioimaging.eu" /> |
| 42 <option value="bcyx">bcyx</option> | 42 <option value="bcyx">bcyx</option> |
| 43 <option value="byxc">byxc</option> | 43 <option value="byxc">byxc</option> |
| 44 </param> | 44 </param> |
| 45 </inputs> | 45 </inputs> |
| 46 <outputs> | 46 <outputs> |
| 47 <data format="tif" name="output_predicted_image" from_work_dir="output_predicted_image.tif" label="Predicted image"></data> | 47 <data format="tiff" name="output_predicted_image" from_work_dir="output_predicted_image.tiff" label="Predicted image"></data> |
| 48 <data format="npy" name="output_predicted_image_matrix" from_work_dir="output_predicted_image_matrix.npy" label="Predicted image tensor"></data> | 48 <data format="npy" name="output_predicted_image_matrix" from_work_dir="output_predicted_image_matrix.npy" label="Predicted image tensor"></data> |
| 49 </outputs> | 49 </outputs> |
| 50 <tests> | 50 <tests> |
| 51 <test> | 51 <test> |
| 52 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://zenodo.org/api/records/6647674/files/weights-torchscript.pt/content"/> | 52 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://zenodo.org/api/records/6647674/files/weights-torchscript.pt/content"/> |
| 53 <param name="input_image_file" value="input_image_file.tif" location="https://zenodo.org/api/records/6647674/files/sample_input_0.tif/content"/> | 53 <param name="input_image_file" value="input_image_file.tif" location="https://zenodo.org/api/records/6647674/files/sample_input_0.tif/content"/> |
| 54 <param name="input_image_input_size" value="256,256,1,1"/> | 54 <param name="input_image_input_size" value="256,256,1,1"/> |
| 55 <param name="input_image_input_axes" value="bcyx"/> | 55 <param name="input_image_input_axes" value="bcyx"/> |
| 56 <output name="output_predicted_image" ftype="tif"> | 56 <output name="output_predicted_image" ftype="tiff"> |
| 57 <assert_contents> | 57 <assert_contents> |
| 58 <has_size size="524846" delta="110" /> | 58 <has_size size="524846" delta="110" /> |
| 59 </assert_contents> | 59 </assert_contents> |
| 60 </output> | 60 </output> |
| 61 <output name="output_predicted_image_matrix" ftype="npy"> | 61 <output name="output_predicted_image_matrix" ftype="npy"> |
| 67 <test> | 67 <test> |
| 68 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://zenodo.org/api/records/6647674/files/weights-torchscript.pt/content"/> | 68 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://zenodo.org/api/records/6647674/files/weights-torchscript.pt/content"/> |
| 69 <param name="input_image_file" value="input_nucleisegboundarymodel.png"/> | 69 <param name="input_image_file" value="input_nucleisegboundarymodel.png"/> |
| 70 <param name="input_image_input_size" value="256,256,1,1"/> | 70 <param name="input_image_input_size" value="256,256,1,1"/> |
| 71 <param name="input_image_input_axes" value="bcyx"/> | 71 <param name="input_image_input_axes" value="bcyx"/> |
| 72 <output name="output_predicted_image" ftype="tif"> | 72 <output name="output_predicted_image" ftype="tiff"> |
| 73 <assert_contents> | 73 <assert_contents> |
| 74 <has_size size="524846" delta="110" /> | 74 <has_size size="524846" delta="110" /> |
| 75 </assert_contents> | 75 </assert_contents> |
| 76 </output> | 76 </output> |
| 77 <output name="output_predicted_image_matrix" ftype="npy"> | 77 <output name="output_predicted_image_matrix" ftype="npy"> |
| 83 <test> | 83 <test> |
| 84 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/torchscript_tracing.pt"/> | 84 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/torchscript_tracing.pt"/> |
| 85 <param name="input_image_file" value="input_image_file.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/sample_input_0.tif"/> | 85 <param name="input_image_file" value="input_image_file.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/sample_input_0.tif"/> |
| 86 <param name="input_image_input_size" value="128,128,100,1"/> | 86 <param name="input_image_input_size" value="128,128,100,1"/> |
| 87 <param name="input_image_input_axes" value="bczyx"/> | 87 <param name="input_image_input_axes" value="bczyx"/> |
| 88 <output name="output_predicted_image" ftype="tif"> | 88 <output name="output_predicted_image" ftype="tiff"> |
| 89 <assert_contents> | 89 <assert_contents> |
| 90 <has_size size="6572778" delta="100" /> | 90 <has_size size="6572778" delta="100" /> |
| 91 </assert_contents> | 91 </assert_contents> |
| 92 </output> | 92 </output> |
| 93 <output name="output_predicted_image_matrix" ftype="npy"> | 93 <output name="output_predicted_image_matrix" ftype="npy"> |
| 99 <test> | 99 <test> |
| 100 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/torchscript_tracing.pt"/> | 100 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/torchscript_tracing.pt"/> |
| 101 <param name="input_image_file" value="input_3d-unet-arabidopsis-apical-stem-cells.png" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/raw.png"/> | 101 <param name="input_image_file" value="input_3d-unet-arabidopsis-apical-stem-cells.png" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/raw.png"/> |
| 102 <param name="input_image_input_size" value="128,128,100,1"/> | 102 <param name="input_image_input_size" value="128,128,100,1"/> |
| 103 <param name="input_image_input_axes" value="bczyx"/> | 103 <param name="input_image_input_axes" value="bczyx"/> |
| 104 <output name="output_predicted_image" ftype="tif"> | 104 <output name="output_predicted_image" ftype="tiff"> |
| 105 <assert_contents> | 105 <assert_contents> |
| 106 <has_size size="6572778" delta="100" /> | 106 <has_size size="6572778" delta="100" /> |
| 107 </assert_contents> | 107 </assert_contents> |
| 108 </output> | 108 </output> |
| 109 <output name="output_predicted_image_matrix" ftype="npy"> | 109 <output name="output_predicted_image_matrix" ftype="npy"> |
| 115 <test> | 115 <test> |
| 116 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/organized-badger/1/files/weights-torchscript.pt"/> | 116 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/organized-badger/1/files/weights-torchscript.pt"/> |
| 117 <param name="input_image_file" value="input_platynereisemnucleisegmentationboundarymodel.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/organized-badger/1/files/sample_input_0.tif"/> | 117 <param name="input_image_file" value="input_platynereisemnucleisegmentationboundarymodel.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/organized-badger/1/files/sample_input_0.tif"/> |
| 118 <param name="input_image_input_size" value="256,256,32,1"/> | 118 <param name="input_image_input_size" value="256,256,32,1"/> |
| 119 <param name="input_image_input_axes" value="bczyx"/> | 119 <param name="input_image_input_axes" value="bczyx"/> |
| 120 <output name="output_predicted_image" ftype="tif"> | 120 <output name="output_predicted_image" ftype="tiff"> |
| 121 <assert_contents> | 121 <assert_contents> |
| 122 <has_size size="16789714" delta="100" /> | 122 <has_size size="16789714" delta="100" /> |
| 123 </assert_contents> | 123 </assert_contents> |
| 124 </output> | 124 </output> |
| 125 <output name="output_predicted_image_matrix" ftype="npy"> | 125 <output name="output_predicted_image_matrix" ftype="npy"> |
| 131 <test> | 131 <test> |
| 132 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/thoughtful-turtle/1/files/torchscript_tracing.pt"/> | 132 <param name="input_imaging_model" value="input_imaging_model.zip" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/thoughtful-turtle/1/files/torchscript_tracing.pt"/> |
| 133 <param name="input_image_file" value="input_3d-unet-lateral-root-primordia-cells.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/thoughtful-turtle/1/files/sample_input_0.tif"/> | 133 <param name="input_image_file" value="input_3d-unet-lateral-root-primordia-cells.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/thoughtful-turtle/1/files/sample_input_0.tif"/> |
| 134 <param name="input_image_input_size" value="128,128,100,1"/> | 134 <param name="input_image_input_size" value="128,128,100,1"/> |
| 135 <param name="input_image_input_axes" value="bczyx"/> | 135 <param name="input_image_input_axes" value="bczyx"/> |
| 136 <output name="output_predicted_image" ftype="tif"> | 136 <output name="output_predicted_image" ftype="tiff"> |
| 137 <assert_contents> | 137 <assert_contents> |
| 138 <has_size size="6572778" delta="100" /> | 138 <has_size size="6572778" delta="100" /> |
| 139 </assert_contents> | 139 </assert_contents> |
| 140 </output> | 140 </output> |
| 141 <output name="output_predicted_image_matrix" ftype="npy"> | 141 <output name="output_predicted_image_matrix" ftype="npy"> |