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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
  ~  GNU General Public License for more details.
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<jsap>
    <parameters>

        <flaggedOption>
            <id>input</id>
            <longFlag>input</longFlag>
            <shortFlag>i</shortFlag>
            <stringParser>
                <classname>StringStringParser</classname>
            </stringParser>
            <required>true</required>
            <help>Name of the input compact-reads file.</help>
        </flaggedOption>
        <unflaggedOption>
            <id>process-part-command</id>
            <stringParser>
                <classname>StringStringParser</classname>
            </stringParser>
            <greedy>true</greedy>
            <required>true</required>
            <help>Command to execute in parallel for each piece of the input. The symbol %read.fastq% will be
                replaced with the filename for the fastq file of each piece. The symbol %tmp1% will be
                available with a valid and distinct filename for each part to write temporary content.
                The symbol %output% will be available with a valid filename to write the output of this part
                (pre-concat output). When the --paired argument is given, the symbol %pair.fastq% will be
                replaced with the filename for the fastq file corresponding to pair sequences.
            </help>
        </unflaggedOption>

        <switch>
            <id>paired</id>
            <longFlag>paired</longFlag>

            <defaults>false</defaults>
            <help>When this switch is provided, extract pairs from the compact reads input and generate
                %pair.fastq% symbols.
            </help>
        </switch>
        <flaggedOption>
            <id>num-parts</id>
            <longFlag>num-parts</longFlag>
            <shortFlag>n</shortFlag>
            <stringParser>
                <classname>IntegerStringParser</classname>
            </stringParser>
            <required>true</required>
            <help>Number of parts needed, n.
            </help>
        </flaggedOption>
        <flaggedOption>
            <id>output</id>
            <longFlag>output</longFlag>
            <shortFlag>o</shortFlag>
            <stringParser>
                <classname>StringStringParser</classname>
            </stringParser>
            <required>true</required>
            <help>output filename, where compact-alignment will be written.</help>
        </flaggedOption>
    </parameters>
</jsap>
