# HG changeset patch
# User imgteam
# Date 1549741349 18000
# Node ID 0bbe34198e242bfbda1d93e435bd711f530fa387

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

diff -r 000000000000 -r 0bbe34198e24 permutate_axis.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/permutate_axis.py	Sat Feb 09 14:42:29 2019 -0500
@@ -0,0 +1,40 @@
+import argparse
+import sys
+import warnings
+import numpy as np
+import skimage.io
+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
+        if axis == 0:
+            a_slice = raw_image[i]
+        elif axis == 1:
+            a_slice = raw_image[:,i]
+        elif axis == 2:
+            a_slice = raw_image[:,:,i]
+        elif axis == 3:
+            a_slice = raw_image[:,:,:,i]
+        elif axis == 4:
+            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')
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
+    parser.add_argument('out_file', type=argparse.FileType('w'), help='out file (TIFF)')
+    parser.add_argument('permutate', help='new channel order', default='0,1,2', type=str)
+    parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis')
+    args = parser.parse_args()
+
+    permutate = [int(item) for item in args.permutate.split(',')]
+    permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)
diff -r 000000000000 -r 0bbe34198e24 permutate_axis.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/permutate_axis.xml	Sat Feb 09 14:42:29 2019 -0500
@@ -0,0 +1,36 @@
+<tool id="ip_permutate_axis" name="Permutate image" version="0.1">
+    <description>along an axis</description>
+    <requirements>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+    </requirements>
+    <command>
+    <![CDATA[
+    python '$__tool_directory__/permutate_axis.py' '$input' '$output' $permutate --axis $axis
+    ]]>
+    </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">
+            <validator type="regex" message="Input has to be a sequence of axis, separated by commas">([0-4],)+[0-4]</validator>
+        </param>
+        <param name="axis" type="integer" value="0" label="concatenation axis" help="Concatenation axis (0-4)" /><!-- why not have a selection from 0 to 4?-->
+    </inputs>
+    <outputs>
+        <data format="tiff" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="galaxyIcon_noText.tif"/>
+            <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    Permutates the image along a specified axis.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 
+    </citations>
+</tool>
diff -r 000000000000 -r 0bbe34198e24 test-data/galaxyIcon_noText.png
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diff -r 000000000000 -r 0bbe34198e24 test-data/galaxyIcon_noText.tif
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diff -r 000000000000 -r 0bbe34198e24 test-data/res.tif
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