# HG changeset patch
# User imgteam
# Date 1765985657 0
# Node ID ce64e2e4afd2c43a50e03ae93153e2db8e132494
# Parent  21168547d5724adcc1f7dd7971cfeece882e5ea8
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f

diff -r 21168547d572 -r ce64e2e4afd2 permutate_axis.py
--- a/permutate_axis.py	Wed Dec 18 09:58:57 2019 +0000
+++ b/permutate_axis.py	Wed Dec 17 15:34:17 2025 +0000
@@ -1,32 +1,34 @@
 import argparse
-import sys
 import warnings
+
 import numpy as np
 import skimage.io
-import skimage.util 
+import skimage.util
+
 
 def permutate_axis(input_image_path, output_image_path, axis, permutate):
     images = []
     raw_image = skimage.io.imread(input_image_path, plugin='tifffile')
     for i in permutate:
-        # TODO generalise 
+        # TODO generalise
         if axis == 0:
             a_slice = raw_image[i]
         elif axis == 1:
-            a_slice = raw_image[:,i]
+            a_slice = raw_image[:, i]
         elif axis == 2:
-            a_slice = raw_image[:,:,i]
+            a_slice = raw_image[:, :, i]
         elif axis == 3:
-            a_slice = raw_image[:,:,:,i]
+            a_slice = raw_image[:, :, :, i]
         elif axis == 4:
-            a_slice = raw_image[:,:,:,:,i]
+            a_slice = raw_image[:, :, :, :, i]
         images.append(np.expand_dims(a_slice, axis))
 
     res = np.concatenate(images, axis)
     with warnings.catch_warnings():
-    	warnings.simplefilter("ignore")
-    	res = skimage.util.img_as_uint(res) #Attention: precision loss
-    	skimage.io.imsave(output_image_path, res, plugin='tifffile')
+        warnings.simplefilter("ignore")
+        res = skimage.util.img_as_uint(res)  # Attention: precision loss
+        skimage.io.imsave(output_image_path, res, plugin='tifffile')
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
diff -r 21168547d572 -r ce64e2e4afd2 permutate_axis.xml
--- a/permutate_axis.xml	Wed Dec 18 09:58:57 2019 +0000
+++ b/permutate_axis.xml	Wed Dec 17 15:34:17 2025 +0000
@@ -1,5 +1,11 @@
-<tool id="ip_permutate_axis" name="Permutate image" version="0.2"> 
-    <description>along an axis</description>
+<tool id="ip_permutate_axis" name="Permutate image axes" version="0.2-2">
+    <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="1.15.4">numpy</requirement>
@@ -9,7 +15,7 @@
     <![CDATA[
     python '$__tool_directory__/permutate_axis.py' '$input' '$output' $permutate --axis $axis
     ]]>
-    </command> 
+    </command>
     <inputs>
         <param name="input" type="data" format="tiff" label="Binary Image File"/>
         <param name="permutate" type="text" value="0,1,2" label="new channel order">
@@ -22,8 +28,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="galaxyIcon_noText.tif"/>
-            <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
+            <param name="input" value="galaxyIcon_noText.tiff"/>
+            <output name="output" file="res.tiff" ftype="tiff" compare="sim_size"/>
         </test>
     </tests>
     <help>
@@ -32,6 +38,6 @@
     Permutates the image along a specified axis.
     </help>
     <citations>
-        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
     </citations>
 </tool>
diff -r 21168547d572 -r ce64e2e4afd2 test-data/galaxyIcon_noText.tif
Binary file test-data/galaxyIcon_noText.tif has changed
diff -r 21168547d572 -r ce64e2e4afd2 test-data/galaxyIcon_noText.tiff
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diff -r 21168547d572 -r ce64e2e4afd2 test-data/res.tif
Binary file test-data/res.tif has changed
diff -r 21168547d572 -r ce64e2e4afd2 test-data/res.tiff
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