<tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0">
  <description>Extract fastq format reads from SRA data archive.</description>
  <command>fastq-dump --stdout $split $aligned $input > $output </command>
  <version_string>fastq-dump --version</version_string>
  <inputs>
    <param format="sra" name="input" type="data" label="sra archive"/>
    <param format="text" name="split" type="select" value="">
      <label>Split read pairs</label>
      <option value="">No</option>
      <option value="--split-spot">Yes</option>
    </param>
    <param format="text" name="aligned" type="select" value="">
      <label>Specify alignment</label>
      <option value="">All</option>
      <option value="--aligned">Only aligned</option>
      <option value="--unaligned">Only unaligned</option>
    </param>
  </inputs>
  <outputs>
    <data format="fastqsanger" name="output"/>
  </outputs>
  <help>
    This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
  </help>
</tool>