<!--
~ Copyright (C) 2009-2017 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>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <required>true</required>
            <help>The output filename.</help>
        </flaggedOption>

        <flaggedOption>
            <id>chromosome-prefix</id>
            <longFlag>chromosome-prefix</longFlag>
            <required>false</required>
            <help>A prefix to append to chromsome names (e.g., +chr) or to remove (e.g., -chr).</help>
        </flaggedOption>
        <unflaggedOption>
            <id>vcfInput</id>
            <required>true</required>
            <greedy>false</greedy>
            <help>The basenames of the input VCF files to convert.</help>
        </unflaggedOption>
    </parameters>
</jsap>
