# HG changeset patch
# User imgteam
# Date 1549740794 18000
# Node ID 30517f733f7b7df12d026203ecd2205cceb5e9fd

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

diff -r 000000000000 -r 30517f733f7b concat_channels.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concat_channels.py	Sat Feb 09 14:33:14 2019 -0500
@@ -0,0 +1,33 @@
+import argparse
+import sys
+import warnings
+import numpy as np
+import skimage.io
+import skimage.util
+
+def concat_channels(input_image_paths, output_image_path, axis):
+    images = []
+    for image_path in input_image_paths:
+        raw_image = skimage.io.imread(image_path)
+        if len(raw_image.shape) == 2:
+            if axis == 0:
+                raw_image = [raw_image]
+            else:
+                raw_image = np.expand_dims(raw_image, 2)
+        images.append(raw_image)
+    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_files', type=argparse.FileType('r'), nargs='+', help='input file')
+    parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'), help='out file (TIFF)')
+    parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0,2], help='concatenation axis')
+    args = parser.parse_args()
+
+    # print([x.name for x in args.input_files], args.out_file.name, args.axis)
+    concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis)
+    # concat_channels(args.input_files, args.out_file, args.axis)
diff -r 000000000000 -r 30517f733f7b concat_channels.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concat_channels.xml	Sat Feb 09 14:33:14 2019 -0500
@@ -0,0 +1,41 @@
+<tool id="ip_concat_channels" name="Concatenate images" version="0.1">
+    <description></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__/concat_channels.py' 
+        #for $input in $inputs
+            '$input'
+        #end for
+        -o '$output' --axis '$axis'
+    ]]>
+    </command>
+    <inputs>
+        <param name="inputs" type="data" multiple="true" format="tiff,png,jpg,bmp" label="Binary Image Files" help="one or multiple binary image fiels"/>
+        <param name="axis" type="select" label="Concatenation Axis">
+            <option value="0">0</option>
+            <option value="2">2</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tiff" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="sample1.png,sample2.png"/>
+            <param name="axis" value="0"/>
+            <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    This tool concatenates images.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 30517f733f7b test-data/out.tiff
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diff -r 000000000000 -r 30517f733f7b test-data/res.tiff
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diff -r 000000000000 -r 30517f733f7b test-data/sample1.png
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diff -r 000000000000 -r 30517f733f7b test-data/sample2.png
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