Mercurial > repos > imgteam > slice_image

changeset 1:8856a7c85e4c draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:03:25 -0500
parents aacfbd7c4af6
children f312d414f234
files slice_image.py slice_image.xml
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/slice_image.py	Sat Feb 09 14:46:50 2019 -0500
+++ b/slice_image.py	Wed Dec 18 05:03:25 2019 -0500
@@ -8,10 +8,10 @@
 import skimage.util
 import skimage.feature
 from scipy.stats import entropy as scipy_entropy
-
+ 
 def slice_image(input_file, out_folder, label=None, label_out_folder=None, window_size=64, 
                 stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None):
-    #TODO NOT Implemented:process labels
+    #TODO NOT Implemented:process labels 
     # --> label and label_out_folder useless so far
 
     # primarily for testing purposes:
--- a/slice_image.xml	Sat Feb 09 14:46:50 2019 -0500
+++ b/slice_image.xml	Wed Dec 18 05:03:25 2019 -0500
@@ -1,11 +1,12 @@
-<tool id="ip_slice_image" name="Slice Image" version="0.2">
+<tool id="ip_slice_image" name="Slice Image" version="0.3">
     <description>into smaller patches</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="1.1.0">scipy</requirement> -->
+        <requirement type="package" version="1.1.0">scipy</requirement>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
     </requirements>
-    <command> 
+    <command detect_errors="aggressive"> 
         <![CDATA[
         mkdir ./out &&
         python '$__tool_directory__/slice_image.py'