Mercurial > repos > imgteam > count_objects

changeset 1:664232d2a3f7 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:01:56 -0500
parents 895a29ebd0c7
children 5bf8eb50b280
files count_objects.py count_objects.xml
diffstat 2 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/count_objects.py	Sat Feb 09 14:34:18 2019 -0500
+++ b/count_objects.py	Wed Dec 18 05:01:56 2019 -0500
@@ -4,14 +4,14 @@
 import numpy as np
 import os
 import skimage.io
-from skimage.measure import regionprops
+from skimage.measure import regionprops 
 
 parser = argparse.ArgumentParser(description='Count Objects')
 parser.add_argument('input_file', type=argparse.FileType('r'),
                     help='Label input file')
 parser.add_argument('output_file', type=argparse.FileType('w'),
                     help='Tabular output file')
-args = parser.parse_args()
+args = parser.parse_args() 
 
 img_raw = skimage.io.imread(args.input_file.name)
 res = len(regionprops(img_raw))
--- a/count_objects.xml	Sat Feb 09 14:34:18 2019 -0500
+++ b/count_objects.xml	Wed Dec 18 05:01:56 2019 -0500
@@ -3,13 +3,14 @@
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="1.15.4">numpy</requirement>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
     </requirements>
     <command>
     <![CDATA[
         python '$__tool_directory__/count_objects.py' '$input' '$output'
     ]]>
     </command>
-    <inputs>
+    <inputs> 
         <param name="input" type="data" format="tiff" label="Source file" />
     </inputs>
     <outputs>