Mercurial > repos > bgruening > cellpose
changeset 1:1857781df226 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 81c6be8cc2502367ae52bf093b838e9764b22c00
author | bgruening |
---|---|
date | Tue, 11 Feb 2025 14:47:54 +0000 |
parents | 4ddb0af5a806 |
children | |
files | cellpose.xml cp_segmentation.py test-data/img02_cp_masks_chan.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 | 11 files changed, 19 insertions(+), 20 deletions(-) [+] |
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--- a/cellpose.xml Fri Aug 23 08:05:53 2024 +0000 +++ b/cellpose.xml Tue Feb 11 14:47:54 2025 +0000 @@ -1,7 +1,7 @@ -<tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> +<tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02"> <description>with Cellpose</description> <macros> - <token name="@TOOL_VERSION@">3.0.10</token> + <token name="@TOOL_VERSION@">3.1.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="channel"> <option value="0" selected="true">grayscale/None</option> @@ -11,7 +11,7 @@ </xml> </macros> <requirements> - <requirement type="package" version="@TOOL_VERSION@">cellpose</requirement> + <container type="docker">quay.io/biocontainers/cellpose:@TOOL_VERSION@</container> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> @@ -59,7 +59,6 @@ <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)"/> <param argument="rescale" type="float" value="" optional="true" label="If diameter is set to None, and rescale is not None, then rescale is used instead of diameter for resizing image"/> <param argument="invert" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to invert image pixel intensity before running network?"/> </section> @@ -76,40 +75,40 @@ <param name="model_type" value="cyto"/> <param name="chan" value="2"/> <param name="chan2" value="3"/> - <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="image_diff"/> </test> <test expect_num_outputs="2"> <param name="img_in" value="img02.png"/> <param name="model_type" value="cyto2"/> <param name="chan" value="2"/> <param name="chan2" value="3"/> - <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="image_diff"/> </test> <test expect_num_outputs="2"> <param name="img_in" value="img02.png"/> <param name="model_type" value="cyto3"/> <param name="chan" value="2"/> <param name="chan2" value="3"/> - <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="image_diff"/> </test> <test expect_num_outputs="2"> <param name="img_in" value="img02.png"/> <param name="model_type" value="nuclei"/> <param name="chan" value="2"/> <param name="chan2" value="3"/> - <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="image_diff"/> </test> <test expect_num_outputs="2"> <param name="img_in" value="img02.png"/> <param name="model_type" value="cyto"/> <param name="chan" value="2"/> <param name="chan2" value="1"/> - <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_chan.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_chan.png" compare="image_diff"/> </test> <test expect_num_outputs="2"> <param name="img_in" value="img02.png"/> @@ -117,8 +116,8 @@ <param name="chan" value="2"/> <param name="chan2" value="3"/> <param name="diameter" value="50"/> - <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/> </test> <test expect_num_outputs="2"> <param name="img_in" value="img02.png"/> @@ -126,8 +125,8 @@ <param name="model_type" value="cyto"/> <param name="chan" value="2"/> <param name="chan2" value="3"/> - <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="sim_size" delta_frac="0.1"/> - <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="image_diff"/> + <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="image_diff"/> </test> <test expect_num_outputs="1"> <param name="img_in" value="img02.png"/> @@ -135,7 +134,7 @@ <param name="chan" value="2"/> <param name="chan2" value="3"/> <param name="show_segmentation" value="false"/> - <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="sim_size" delta_frac="0.1"/> + <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff"/> </test> </tests> <help>