diff imagej2_analyze_particles_binary_jython_script.py @ 2:da29019170f1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

--- a/imagej2_analyze_particles_binary_jython_script.py	Mon Sep 28 16:41:15 2020 +0000
+++ b/imagej2_analyze_particles_binary_jython_script.py	Sun Nov 05 10:52:33 2023 +0000
@@ -3,8 +3,7 @@
 from ij import IJ
 from ij.plugin.filter import Analyzer
 
-
-OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
+OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
@@ -43,24 +42,24 @@
     IJ.run(input_image_plus_copy, "Make Binary", "")
 
 # Set the options.
-options = ['size=%s' % size]
-circularity_str = '%.3f-%.3f' % (circularity_min, circularity_max)
-options.append('circularity=%s' % circularity_str)
-if show.find('_') >= 0:
-    show_str = '[%s]' % show.replace('_', ' ')
+options = ["size=%s" % size]
+circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
+options.append("circularity=%s" % circularity_str)
+if show.find("_") >= 0:
+    show_str = "[%s]" % show.replace("_", " ")
 else:
     show_str = show
-options.append('show=%s' % show_str)
+options.append("show=%s" % show_str)
 if display_results:
-    options.append('display')
+    options.append("display")
     if not all_results:
-        options.append('summarize')
+        options.append("summarize")
 if exclude_edges:
-    options.append('exclude')
+    options.append("exclude")
 if include_holes:
-    options.append('include')
+    options.append("include")
 # Always run "in_situ".
-options.append('in_situ')
+options.append("in_situ")
 
 # Run the command.
 IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))