old_contents: #!/usr/bin/env python
  import argparse
  import shutil
  import operator
  
  import icqsol_utils
  from icqsol.shapes.icqShapeManager import ShapeManager
  
  # Parse Command Line.
  parser = argparse.ArgumentParser()
  parser.add_argument('--input', dest='input', help='Shape dataset selected from history')
  parser.add_argument('--input_file_format_and_type', dest='input_file_format_and_type', help='Input file format and type')
  parser.add_argument('--input_dataset_type', dest='input_dataset_type', help='Input dataset_type')
  parser.add_argument('--rotation_degrees', dest='rotation_degrees', type=float, default=0.0, help='Rotation angle in degrees')
  parser.add_argument('--rotation_axis_x', dest='rotation_axis_x', type=float, default=1.0, help='X coordinate of rotation axis')
  parser.add_argument('--rotation_axis_y', dest='rotation_axis_y', type=float, default=0.0, help='Y coordinate of rotation axis')
  parser.add_argument('--rotation_axis_z', dest='rotation_axis_z', type=float, default=0.0, help='Z coordinate of rotation axis')
  parser.add_argument('--output', dest='output', help='Output file name')
  parser.add_argument('--output_vtk_type', dest='output_vtk_type', default='ascii', help='Output VTK type')
  
  args = parser.parse_args()
  
  # Get the format of the input - either vtk or ply.
  input_format, input_file_type = icqsol_utils.get_format_and_type(args.input_file_format_and_type)
  tmp_dir = icqsol_utils.get_temp_dir()
  
  # Instantiate a ShapeManager for loading the input.
  if input_format == icqsol_utils.VTK:
      shape_mgr = ShapeManager(file_format=input_format, vtk_dataset_type=args.input_dataset_type)
  else:
      shape_mgr = ShapeManager(file_format=input_format)
  
  # Get the vtk polydata from the input dataset.
  vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input)
  
  # Only rotate if the axis has some non-zero coordinates.
  # FIXME: this should be handled in a Galaxy tool validator.
  axis = (args.rotation_axis_x, args.rotation_axis_y, args.rotation_axis_z)
  if reduce(operator.mul, axis) != 0.0:
      # Rotate (in place operation).
      shape_mgr.rotateVtkPolyData(vtk_poly_data, angleDeg=args.rotation_degrees, axis=axis)
  
  output_format, output_file_type = icqsol_utils.get_format_and_type(args.output_vtk_type)
  
  # Save the output.
  tmp_dir = icqsol_utils.get_temp_dir()
  tmp_output_path = icqsol_utils.get_temporary_file_path(tmp_dir, icqsol_utils.VTK)
  shape_mgr.saveVtkPolyData(vtk_poly_data, file_name=tmp_output_path, file_type=output_file_type)
  shutil.move(tmp_output_path, args.output)
  
new_contents: #!/usr/bin/env python
  import argparse
  import shutil
  import operator
  
  import icqsol_utils
  
  # Parse Command Line.
  parser = argparse.ArgumentParser()
  parser.add_argument('--input', dest='input', help='Shape dataset selected from history')
  parser.add_argument('--input_file_format_and_type', dest='input_file_format_and_type', help='Input file format and type')
  parser.add_argument('--input_dataset_type', dest='input_dataset_type', help='Input dataset_type')
  parser.add_argument('--rotation_degrees', dest='rotation_degrees', type=float, default=0.0, help='Rotation angle in degrees')
  parser.add_argument('--rotation_axis_x', dest='rotation_axis_x', type=float, default=1.0, help='X coordinate of rotation axis')
  parser.add_argument('--rotation_axis_y', dest='rotation_axis_y', type=float, default=0.0, help='Y coordinate of rotation axis')
  parser.add_argument('--rotation_axis_z', dest='rotation_axis_z', type=float, default=0.0, help='Z coordinate of rotation axis')
  parser.add_argument('--output', dest='output', help='Output file name')
  parser.add_argument('--output_vtk_type', dest='output_vtk_type', default='ascii', help='Output VTK type')
  
  args = parser.parse_args()
  
  # Get the format of the input - either vtk or ply.
  input_format, input_file_type = icqsol_utils.get_format_and_type(args.input_file_format_and_type)
  tmp_dir = icqsol_utils.get_temp_dir()
  
  # Instantiate a ShapeManager for loading the input.
  shape_mgr = icqsol_utils.get_shape_manager(input_format, args.input_dataset_type)
  
  # Get the vtk polydata from the input dataset.
  vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input)
  
  # Only rotate if the axis has some non-zero coordinates.
  # FIXME: this should be handled in a Galaxy tool validator.
  axis = (args.rotation_axis_x, args.rotation_axis_y, args.rotation_axis_z)
  if reduce(operator.mul, axis) != 0.0:
      # Rotate (in place operation).
      shape_mgr.rotateVtkPolyData(vtk_poly_data, angleDeg=args.rotation_degrees, axis=axis)
  
  output_format, output_file_type = icqsol_utils.get_format_and_type(args.output_vtk_type)
  
  # Save the output.
  tmp_dir = icqsol_utils.get_temp_dir()
  tmp_output_path = icqsol_utils.get_temporary_file_path(tmp_dir, icqsol_utils.VTK)
  shape_mgr.saveVtkPolyData(vtk_poly_data, file_name=tmp_output_path, file_type=output_file_type)
  shutil.move(tmp_output_path, args.output)
  
subject: Update icqsol_rotate_shape with icqsol_utils encapsulation.