comparison sam_dump.xml @ 11:cdba74ec9eca draft

updated sra_toolkit dependency in <requirements>

10:3b814b721838

      <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>

  </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 [e-mail] for support and bug reports.
  </help>

11:cdba74ec9eca

      <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 as well as aligned 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>

  </inputs>
  <outputs>
    <data format="sam" name="output"/>
  </outputs>
  <requirements>
    <requirement type="package" version="2.3.2-4">sra_toolkit</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 [e-mail] for support and bug reports.
  </help>