original_docstring: 
          
          Wrap toil-vg index. Files passed are copied from store instead of
          computed. If "SKIP" is used as a filename, don't create or copy that
          index. Otherwise, pass None as a filename to compute that index.
          
          
docstring: Wrap toil-vg index. Files passed are copied from store instead of
  computed. If "SKIP" is used as a filename, don't create or copy that
  index. Otherwise, pass None as a filename to compute that index.
docstring_tokens: Wrap toil - vg index . Files passed are copied from store instead of computed . If " SKIP " is used as a filename don ' t create or copy that index . Otherwise pass None as a filename to compute that index .
code: def _toil_vg_index(self, chrom, graph_path, xg_path, gcsa_path, misc_opts, dir_tag, file_tag):
          """
          
          Wrap toil-vg index. Files passed are copied from store instead of
          computed. If "SKIP" is used as a filename, don't create or copy that
          index. Otherwise, pass None as a filename to compute that index.
          
          """
          job_store = self._jobstore(dir_tag)
          out_store = self._outstore(dir_tag)
          opts = ' '.join(self._toil_vg_io_opts()) + ' '
          if self.vg_docker:
              opts += '--vg_docker {} '.format(self.vg_docker)
          if self.container:
              opts += '--container {} '.format(self.container)
          if chrom:
              opts += '--chroms {} '.format(chrom)
          if graph_path:
              opts += '--graphs {} '.format(graph_path)
          if xg_path:
              if xg_path != "SKIP":
                  self._get_remote_file(xg_path, os.path.join(out_store, os.path.basename(xg_path)))
          else:
              opts += '--xg_index '
          if gcsa_path:
              if gcsa_path != "SKIP":
                  self._get_remote_file(gcsa_path, os.path.join(out_store, os.path.basename(gcsa_path)))
                  self._get_remote_file(gcsa_path + '.lcp', os.path.join(out_store, os.path.basename(gcsa_path) + '.lcp'))
          else:
              opts += '--gcsa_index '
          opts += '--index_name {}'.format(file_tag)
          if misc_opts:
              opts += ' {} '.format(misc_opts)
          
          cmd = 'toil-vg index {} {} {}'.format(job_store, out_store, opts)
          sys.stderr.write("Running toil-vg indexing: {}".format(cmd))
          
          subprocess.check_call(cmd, shell=True)
code_tokens: def _toil_vg_index ( self , chrom , graph_path , xg_path , gcsa_path , misc_opts , dir_tag , file_tag ) : job_store = self . _jobstore ( dir_tag ) out_store = self . _outstore ( dir_tag ) opts = ' ' . join ( self . _toil_vg_io_opts ( ) ) + ' ' if self . vg_docker : opts += '--vg_docker {} ' . format ( self . vg_docker ) if self . container : opts += '--container {} ' . format ( self . container ) if chrom : opts += '--chroms {} ' . format ( chrom ) if graph_path : opts += '--graphs {} ' . format ( graph_path ) if xg_path : if xg_path != "SKIP" : self . _get_remote_file ( xg_path , os . path . join ( out_store , os . path . basename ( xg_path ) ) ) else : opts += '--xg_index ' if gcsa_path : if gcsa_path != "SKIP" : self . _get_remote_file ( gcsa_path , os . path . join ( out_store , os . path . basename ( gcsa_path ) ) ) self . _get_remote_file ( gcsa_path + '.lcp' , os . path . join ( out_store , os . path . basename ( gcsa_path ) + '.lcp' ) ) else : opts += '--gcsa_index ' opts += '--index_name {}' . format ( file_tag ) if misc_opts : opts += ' {} ' . format ( misc_opts ) cmd = 'toil-vg index {} {} {}' . format ( job_store , out_store , opts ) sys . stderr . write ( "Running toil-vg indexing: {}" . format ( cmd ) ) subprocess . check_call ( cmd , shell = True )
short_docstring: Wrap toil-vg index.
short_docstring_tokens: Wrap toil - vg index .
comment: """
          
          Wrap toil-vg index. Files passed are copied from store instead of
          computed. If "SKIP" is used as a filename, don't create or copy that
          index. Otherwise, pass None as a filename to compute that index.
          
          """