# HG changeset patch
# User bgruening
# Date 1715897124 0
# Node ID eda6dfae9617f3eece05734b945c0667f9e646c7
# Parent  030bfe6065d932d60200395b6f1dc7e5eeafec73
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 7e5c9f013821c8905f2c9c452a1f00891e3a0cfd

diff -r 030bfe6065d9 -r eda6dfae9617 cellpose.xml
--- 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)"/>
diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_masks_chan.tif
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_masks_cyto2.tif
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_masks_cyto3.tif
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_masks_diameter.tif
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_masks_gpu.tif
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_masks_nuclei.tif
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_segm_chan.png
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_segm_cyto.png
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_segm_cyto2.png
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diff -r 030bfe6065d9 -r eda6dfae9617 test-data/img02_cp_segm_nuclei.png
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