Mercurial > repos > bgruening > cellpose
changeset 2:eda6dfae9617 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 7e5c9f013821c8905f2c9c452a1f00891e3a0cfd
| author | bgruening |
|---|---|
| date | Thu, 16 May 2024 22:05:24 +0000 |
| parents | 030bfe6065d9 |
| children | |
| files | cellpose.xml test-data/img02_cp_masks_chan.tif test-data/img02_cp_masks_cyto.tif test-data/img02_cp_masks_cyto2.tif test-data/img02_cp_masks_cyto3.tif test-data/img02_cp_masks_diameter.tif test-data/img02_cp_masks_gpu.tif test-data/img02_cp_masks_nuclei.tif test-data/img02_cp_segm_chan.png test-data/img02_cp_segm_cyto.png test-data/img02_cp_segm_cyto2.png test-data/img02_cp_segm_cyto3.png test-data/img02_cp_segm_diameter.png test-data/img02_cp_segm_gpu.png test-data/img02_cp_segm_nuclei.png |
| diffstat | 15 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/cellpose.xml Sat Mar 02 13:35:21 2024 +0000 +++ b/cellpose.xml Thu May 16 22:05:24 2024 +0000 @@ -1,8 +1,8 @@ <tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description>with Cellpose</description> <macros> - <token name="@TOOL_VERSION@">3.0.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">3.0.8</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="channel"> <option value="0" selected="true">grayscale/None</option> <option value="1">red</option> @@ -11,7 +11,7 @@ </xml> </macros> <requirements> - <container type="docker">biocontainers/cellpose:3.0.1_cv1</container> + <requirement type="package" version="@TOOL_VERSION@">cellpose</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> @@ -22,7 +22,7 @@ export CELLPOSE_LOCAL_MODELS_PATH='cellpose_models' && mkdir -p segmentation && ln -s '${img_in}' ./image.${img_in.ext} && - + python '$__tool_directory__/cp_segmentation.py' --inputs '$inputs' --img_path ./image.${img_in.ext} @@ -56,7 +56,7 @@ help="Interpolated flows at the true image size. This option will create smoother ROIs when the cells are large but will be slower in case"/> <param argument="flow_threshold" type="float" min="0" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/> <param argument="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/> - <param argument="niter" type="integer" min="0" value="0" label="Number of iterations" + <param argument="niter" type="integer" min="0" value="0" label="Number of iterations" help="By defalut, sets the number of iterations to be proportional to the ROI diameter. For longer ROIs, more iterations might be needed."/> <param argument="do_3D" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to run 3D segmentation on 4D image input?"/> <param argument="tile" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Tiles image for test time augmentation and to ensure GPU memory usage limited (recommended)"/>