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  ~ 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.
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<jsap>
    <parameters>
        <flaggedOption>
            <id>input</id>
            <shortFlag>i</shortFlag>
            <longFlag>input</longFlag>
            <required>true</required>
            <help>Input transcripts FASTA file. The transcript-ids and gene-ids need to be embedded into the Fasta reference in the header/comment lines. It is assumed that the comment / header line for each sequence will be in the format ">TRANSCRIPT_ID IGNORED_DATA gene:GENE_ID". For example ">ENST00000400845 cdna:known supercontig::GL000222.1:11792:16670:1 gene:ENSG00000215756" speciefies a transcript-id of "ENST00000400845" and a gene-id of "ENSG00000215756".</help>
        </flaggedOption>
        <flaggedOption>
            <id>output</id>
            <shortFlag>o</shortFlag>
            <longFlag>output</longFlag>
            <required>true</required>
            <help>Base output path / filename. Several files will be created using this base including multiple FASTA files and a config file.</help>
        </flaggedOption>
        <flaggedOption>
            <id>max-entries-per-file</id>
            <shortFlag>n</shortFlag>
            <longFlag>max-entries-per-file</longFlag>
            <required>false</required>
            <stringParser>
                <classname>IntegerStringParser</classname>
            </stringParser>
            <defaults>
                <string>2147483647</string>
            </defaults>
            <help>Maximum number of entries that should be written to any given output file.</help>
        </flaggedOption>
    </parameters>
</jsap>
