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<!--
~ Copyright (C) 2009-2012 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>
<unflaggedOption>
<id>input</id>
<required>true</required>
<greedy>true</greedy>
<help>Tab delimited files to append and perform FDR adjustment on.</help>
</unflaggedOption>
<flaggedOption>
<id>output</id>
<shortFlag>o</shortFlag>
<longFlag>output</longFlag>
<required>true</required>
<help>The file where the combined output will be written. If the filename ends in .gz, the output is
compressed with gzip.
</help>
</flaggedOption>
<flaggedOption>
<id>min-mapping-quality</id>
<shortFlag>q</shortFlag>
<longFlag>min-mapping-quality</longFlag>
<required>false</required>
<stringParser>
<classname>IntegerStringParser</classname>
</stringParser>
<help>The minimum mapping quality that alignments must have to be considered in a tally of the splicing
events. Spliced reads with a mapping quality strictly less than this threshold are ignored.
The default value is 255. The threshold is not applied to reads that do not have a mapping quality field.
</help>
<defaults>
<string>255</string>
</defaults>
</flaggedOption>
</parameters>
</jsap>
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