diff imagej2_skeletonize3d.py @ 1:269923244cc8 draft

planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty

--- a/imagej2_skeletonize3d.py	Tue Aug 04 13:21:32 2015 -0400
+++ b/imagej2_skeletonize3d.py	Wed Aug 26 14:38:34 2015 -0400
@@ -9,9 +9,8 @@
 parser = argparse.ArgumentParser()
 parser.add_argument( '--input', dest='input', help='Path to the input file' )
 parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
+parser.add_argument( '--black_background', dest='black_background', help='Black background' )
 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
-parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
 parser.add_argument( '--output', dest='output', help='Path to the output file' )
 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
 args = parser.parse_args()
@@ -22,8 +21,6 @@
 # extension that points to the Galaxy dataset.  This symlink is used by ImageJ.
 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
-# Set the size of the memory allocation pool used by the JVM.
-memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
 # Define command response buffers.
 tmp_out = tempfile.NamedTemporaryFile().name
 tmp_stdout = open( tmp_out, 'wb' )
@@ -32,11 +29,12 @@
 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
 error_log = tempfile.NamedTemporaryFile( delete=False ).name
 # Build the command line.
-cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script )
+cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
 if cmd is None:
     imagej2_base_utils.stop_err( "ImageJ not found!" )
 cmd += ' %s' % error_log
 cmd += ' %s' % tmp_input_path
+cmd += ' %s' % args.black_background
 cmd += ' %s' % tmp_output_path
 cmd += ' %s' % args.output_datatype
 # Run the command.