<!--
  ~ Copyright (C) 2009-2010 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
  ~  GNU General Public License for more details.
  ~
  ~  You should have received a copy of the GNU General Public License
  ~  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  -->

<jsap>
    <parameters>

        <flaggedOption>
            <id>basename</id>
            <shortFlag>b</shortFlag>
            <longFlag>basename</longFlag>
            <required>false</required>
            <help>The cache basename. The basename will be used to construct the filenames for the cache file constituents. When the basename is not provided, one is constructed by removing the extension(s) of the input file (two extensions are moved when the file ends in .gz).</help>
        </flaggedOption>

        <unflaggedOption>
            <id>input</id>
            <required>true</required>
            <help>The fasta or compact file to convert.</help>
        </unflaggedOption>


    </parameters>
</jsap>
