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  ~ Copyright (C) 2009-2011 Institute for Computational Biomedicine,
  ~                    Weill Medical College of Cornell University
  ~
  ~  This program is free software; you can redistribute it and/or modify
  ~  it under the terms of the GNU General Public License as published by
  ~  the Free Software Foundation; either version 3 of the License, or
  ~  (at your option) any later version.
  ~
  ~  This program is distributed in the hope that it will be useful,
  ~  but WITHOUT ANY WARRANTY; without even the implied warranty of
  ~  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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  -->

<jsap>
    <parameters>

      <unflaggedOption>
            <id>input</id>
            <stringParser>
                <classname>StringStringParser</classname>
            </stringParser>
            <greedy>true</greedy>  
          <required>true</required>
            <help>Name of the alignment files to upgrade.</help>
      </unflaggedOption>
       <!--switch>
            <id>check</id>
            <longFlag>check</longFlag>
            <help>Check the alignemnt after upgrading </help>
        </switch-->
    </parameters>
</jsap>
