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changeset 1:1857781df226 draft default tip

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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(-) [+]
line wrap: on
line diff
--- 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>
--- a/cp_segmentation.py	Fri Aug 23 08:05:53 2024 +0000
+++ b/cp_segmentation.py	Tue Feb 11 14:47:54 2025 +0000
@@ -23,7 +23,7 @@
         Folder to save the outputs.
     """
     warnings.simplefilter('ignore')
-
+    np.random.seed(42)
     with open(inputs, 'r') as param_handler:
         params = json.load(param_handler)
 
Binary file test-data/img02_cp_masks_chan.tif has changed
Binary file test-data/img02_cp_masks_nuclei.tif has changed
Binary file test-data/img02_cp_segm_chan.png has changed
Binary file test-data/img02_cp_segm_cyto.png has changed
Binary file test-data/img02_cp_segm_cyto2.png has changed
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Binary file test-data/img02_cp_segm_diameter.png has changed
Binary file test-data/img02_cp_segm_gpu.png has changed
Binary file test-data/img02_cp_segm_nuclei.png has changed