<tool id="sam_dump" name="Extract SAM" version="1.0.0">
  <description> format reads from NCBI SRA.</description>
  <command>sam-dump $header $aligned $primary $input > $output</command>
  <version_string>sam-dump --version</version_string>
  <inputs>
    <param format="sra" name="input" type="data" label="sra archive"/>
    <param format="text" name="header" type="select" value="">
      <label>Output SAM header</label>
      <option value="--header">Yes</option>
      <option value="--no-header">No</option>
    </param>
    <param format="text" name="aligned" type="select" value="">
      <label>Output unaligned reads</label>
      <option value="">No</option>
      <option value="--unaligned">Yes</option>
    </param>
    <param format="text" name="primary" type="select" value="">
      <label>Output only primary aligments</label>
      <option value="">No</option>
      <option value="--primary">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="sam" name="output"/>
  </outputs>
  <requirements>
    <requirement type="binary">sam-dump</requirement>
  </requirements>
  <help>
    This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
  </help>
</tool>