# HG changeset patch
# User imgteam
# Date 1645895693 0
# Node ID 22e573b7dcb1b5d152b7e4e60c88ef2d89b24865
# Parent  8ad39f4935871dc5e32174e24deba6eab1e89fc7
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"

diff -r 8ad39f493587 -r 22e573b7dcb1 overlay_segmentation_mask.py
--- a/overlay_segmentation_mask.py	Mon Jul 22 05:03:51 2019 -0400
+++ b/overlay_segmentation_mask.py	Sat Feb 26 17:14:53 2022 +0000
@@ -1,20 +1,17 @@
 import argparse
-import sys
-import os
 
 import matplotlib
-matplotlib.use('Agg')
 import matplotlib.pyplot as plt
+import skimage.io
+import skimage.measure
 
-#TODO make importable by python script
-
-import skimage.io
-import skimage.measure 
+matplotlib.use('Agg')
+# TODO make importable by python script
 
 parser = argparse.ArgumentParser()
 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
 parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file')
-parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy
+parser.add_argument('out_file', type=str, help='out file (PNG)')  # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy
 parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale')
 parser.add_argument('--label', dest='label', action='store_true', help='plot label')
 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
diff -r 8ad39f493587 -r 22e573b7dcb1 overlay_segmentation_mask.xml
--- a/overlay_segmentation_mask.xml	Mon Jul 22 05:03:51 2019 -0400
+++ b/overlay_segmentation_mask.xml	Sat Feb 26 17:14:53 2022 +0000
@@ -1,11 +1,9 @@
-<tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.6"> 
+<tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.7" profile="20.05"> 
     <description>Overlay Segmentation Mask</description>
     <requirements>
-        <requirement type="package" version="0.14.2">scikit-image</requirement> 
-        <requirement type="package" version="3.0.2">matplotlib</requirement>
-        <requirement type="package" version="5.3.0">pillow</requirement>
-        <requirement type="package" version="0.15.1">tifffile</requirement>
-        <requirement type="package" version="1.16.0">numpy</requirement>
+        <requirement type="package" version="0.18.1">scikit-image</requirement> 
+        <requirement type="package" version="3.3.4">matplotlib</requirement>
+        <requirement type="package" version="1.20.2">numpy</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         python '$__tool_directory__/overlay_segmentation_mask.py'
@@ -53,8 +51,9 @@
     **What it does**
 
     This tool overlays a segmentation mask over an image.
+
+    Note: This tool is deprecated and may not be supported in future. Please use the tool "Overlay Images" instead.
     </help>
     <citations>
-        <citation type="doi">10.7717/peerj.453</citation>
     </citations>
 </tool>
diff -r 8ad39f493587 -r 22e573b7dcb1 test-data/outt.png
Binary file test-data/outt.png has changed