Mercurial > repos > imgteam > wsi_extract_top_view

changeset 1:cfe88c6041e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:03:44 -0500
parents a1d02d2e814a
children 3bd767eee603
files wsi_extract_top_view.py wsi_extract_top_view.xml
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/wsi_extract_top_view.py	Sat Feb 09 14:49:03 2019 -0500
+++ b/wsi_extract_top_view.py	Wed Dec 18 05:03:44 2019 -0500
@@ -4,7 +4,7 @@
 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]
@@ -18,5 +18,5 @@
     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)
--- a/wsi_extract_top_view.xml	Sat Feb 09 14:49:03 2019 -0500
+++ b/wsi_extract_top_view.xml	Wed Dec 18 05:03:44 2019 -0500
@@ -1,12 +1,13 @@
-<tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.1"> 
+<tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.2"> 
     <description>from whole-slice image</description>
-    <requirements> 
+    <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>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
     </requirements>
-    <command> 
+    <command detect_errors="aggressive"> 
         <![CDATA[
         python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output'
         ]]>