diff jython_script.py @ 2:ef4de385bbde draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936

--- a/jython_script.py	Sun Oct 11 13:29:52 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-import jython_utils
-import sys
-from ij import IJ
-
-# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-error_log = sys.argv[ -5 ]
-input = sys.argv[ -4 ]
-direction = sys.argv[ -3 ]
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
-
-# Open the input image file.
-input_image_plus = IJ.openImage( input )
-
-# Create a copy of the image.
-input_image_plus_copy = input_image_plus.duplicate()
-image_processor_copy = input_image_plus_copy.getProcessor()
-
-try:
-    # Run the command.
-    IJ.run( input_image_plus_copy, direction, "" )
-    # Save the ImagePlus object as a new image.
-    IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
-except Exception, e:
-    jython_utils.handle_error( error_log, str( e ) )