| Previous changeset 3:000f171afabb (2025-02-26) Next changeset 5:d5233b9d32bb (2025-04-15) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging commit f038722c21eaa3018e1cef0004ac7bd283d15269 |
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modified:
bioimage_inference.xml main.py |
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| diff -r 000f171afabb -r 4fd6e8b051e9 bioimage_inference.xml --- a/bioimage_inference.xml Wed Feb 26 10:27:36 2025 +0000 +++ b/bioimage_inference.xml Mon Apr 07 14:46:24 2025 +0000 |
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| @@ -2,7 +2,7 @@ <description>with PyTorch</description> <macros> <token name="@TOOL_VERSION@">2.4.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <creator> <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> @@ -44,7 +44,7 @@ </param> </inputs> <outputs> - <data format="tif" name="output_predicted_image" from_work_dir="output_predicted_image.tif" label="Predicted image"></data> + <data format="tiff" name="output_predicted_image" from_work_dir="output_predicted_image.tiff" label="Predicted image"></data> <data format="npy" name="output_predicted_image_matrix" from_work_dir="output_predicted_image_matrix.npy" label="Predicted image tensor"></data> </outputs> <tests> @@ -53,7 +53,7 @@ <param name="input_image_file" value="input_image_file.tif" location="https://zenodo.org/api/records/6647674/files/sample_input_0.tif/content"/> <param name="input_image_input_size" value="256,256,1,1"/> <param name="input_image_input_axes" value="bcyx"/> - <output name="output_predicted_image" ftype="tif"> + <output name="output_predicted_image" ftype="tiff"> <assert_contents> <has_size size="524846" delta="110" /> </assert_contents> @@ -69,7 +69,7 @@ <param name="input_image_file" value="input_nucleisegboundarymodel.png"/> <param name="input_image_input_size" value="256,256,1,1"/> <param name="input_image_input_axes" value="bcyx"/> - <output name="output_predicted_image" ftype="tif"> + <output name="output_predicted_image" ftype="tiff"> <assert_contents> <has_size size="524846" delta="110" /> </assert_contents> @@ -85,7 +85,7 @@ <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"/> <param name="input_image_input_size" value="128,128,100,1"/> <param name="input_image_input_axes" value="bczyx"/> - <output name="output_predicted_image" ftype="tif"> + <output name="output_predicted_image" ftype="tiff"> <assert_contents> <has_size size="6572778" delta="100" /> </assert_contents> @@ -101,7 +101,7 @@ <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"/> <param name="input_image_input_size" value="128,128,100,1"/> <param name="input_image_input_axes" value="bczyx"/> - <output name="output_predicted_image" ftype="tif"> + <output name="output_predicted_image" ftype="tiff"> <assert_contents> <has_size size="6572778" delta="100" /> </assert_contents> @@ -117,7 +117,7 @@ <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"/> <param name="input_image_input_size" value="256,256,32,1"/> <param name="input_image_input_axes" value="bczyx"/> - <output name="output_predicted_image" ftype="tif"> + <output name="output_predicted_image" ftype="tiff"> <assert_contents> <has_size size="16789714" delta="100" /> </assert_contents> @@ -133,7 +133,7 @@ <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"/> <param name="input_image_input_size" value="128,128,100,1"/> <param name="input_image_input_axes" value="bczyx"/> - <output name="output_predicted_image" ftype="tif"> + <output name="output_predicted_image" ftype="tiff"> <assert_contents> <has_size size="6572778" delta="100" /> </assert_contents> |
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| diff -r 000f171afabb -r 4fd6e8b051e9 main.py --- a/main.py Wed Feb 26 10:27:36 2025 +0000 +++ b/main.py Mon Apr 07 14:46:24 2025 +0000 |
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| @@ -141,4 +141,4 @@ pred_numpy = pred_data.detach().numpy() # write predicted TIF image to file - imageio.v3.imwrite("output_predicted_image.tif", pred_numpy, extension=".tif") + imageio.v3.imwrite("output_predicted_image.tiff", pred_numpy, extension=".tiff") |