# HG changeset patch
# User imgteam
# Date 1549741743 18000
# Node ID a1d02d2e814a12e8f9853dff52f6f82bca677d44

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

diff -r 000000000000 -r a1d02d2e814a test-data/CMU-1-Small-Region.svs
Binary file test-data/CMU-1-Small-Region.svs has changed
diff -r 000000000000 -r a1d02d2e814a test-data/out.tif
Binary file test-data/out.tif has changed
diff -r 000000000000 -r a1d02d2e814a wsi_extract_top_view.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wsi_extract_top_view.py	Sat Feb 09 14:49:03 2019 -0500
@@ -0,0 +1,22 @@
+import argparse
+import openslide
+import os
+import fnmatch
+import skimage.io
+import numpy as np
+
+def wsi_extract_top_view(input_path, out_path):
+    img_raw = openslide.OpenSlide(input_path)
+    top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1]
+    img_area = img_raw.read_region((0,0), len(img_raw.level_dimensions)-1, top_size)
+    img_area = np.asarray(img_area, dtype=np.uint8)
+    skimage.io.imsave(out_path, img_area, 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', help='out file')
+    args = parser.parse_args()
+
+    wsi_extract_top_view(args.input_file.name, args.out_file)
diff -r 000000000000 -r a1d02d2e814a wsi_extract_top_view.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wsi_extract_top_view.xml	Sat Feb 09 14:49:03 2019 -0500
@@ -0,0 +1,34 @@
+<tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.1"> 
+    <description>from whole-slice image</description>
+    <requirements> 
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+        <requirement type="package" version="1.1.1">openslide-python</requirement>
+        <requirement type="package" version="0.5">glob2</requirement>
+    </requirements>
+    <command> 
+        <![CDATA[
+        python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output'
+        ]]>
+    </command>
+    <inputs> 
+        <param name="input" type="data" format="svs,svslide,vms,mrxs,tif,tiff" label="Whole Slice Image"/><!--formats taken as listed on https://openslide.org/api/python/-->
+    </inputs>
+    <outputs>
+        <data name="output" format="tiff"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="CMU-1-Small-Region.svs"/>
+            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>