          if hasattr(self.args, 'alignment_format') and self.args.alignment_format:
              dest_format = self.args.alignment_format
          return dest_format
  
      def process(self):
          """ Main processing function of the Align tool """
 
</s> remove         self.alignments = AlignmentData(self.args.alignments_file, dest_format)
 </s> add         if len(self.args.alignments_file) == 1:
            retval = AlignmentData(self.args.alignments_file[0], dest_format)
        else:
            retval = [AlignmentData(a_file, dest_format) for a_file in self.args.alignments_file]
        logger.debug("Alignments: %s", retval)
        return retval </s> remove         self.alignments = alignments
        self.alignments2 = AlignmentData(arguments.alignments_file2, "json")
 </s> add         self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
        logger.debug(dest_format)
          if hasattr(self.args, 'alignment_format') and self.args.alignment_format:
              dest_format = self.args.alignment_format
        logger.debug(dest_format)
          return dest_format
  
      def process(self):
          """ Main processing function of the Align tool """
keep add 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/alignments.py