  
  class Merge():
      """ Merge two alignments files into one """
      def __init__(self, alignments, arguments):
          self.alignments = alignments
          self.alignments2 = AlignmentData(arguments.alignments_file2, "json")
  
      def process(self):
          """Process the alignments file merge """
          logger.info("[MERGE ALIGNMENTS]")  # Tidy up cli output
          skip_count = 0
 
</s> remove                     "\n'merge': Merge multiple alignment files into one. Specify the main"
                    "\n\talignments file with the -a flag and the file to be merged with the"
                    "\n\t-a2 flag."
 </s> add                     "\n'merge': Merge multiple alignment files into one. Specify a space "
                    "\n\tseparated list of alignments files with the -a flag."
        self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
  
  class Merge():
      """ Merge two alignments files into one """
      def __init__(self, alignments, arguments):
        self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
        self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
  
      def process(self):
          """Process the alignments file merge """
          logger.info("[MERGE ALIGNMENTS]")  # Tidy up cli output
          skip_count = 0
keep keep keep keep replace replace keep keep keep keep keep
 Alignments Tool: Allow merging of many alignments file

Adds multi select functionality to GUI, meaning multiple alignments files can now be selected for merging.

Extract: nFilter, Filter now have a file dialog in gui for selecting 1/multiple files 
tools/lib_alignments/jobs.py