view fastq_dump.xml @ 11:cdba74ec9eca draft

updated sra_toolkit dependency in <requirements>

<tool id="fastq_dump" name="Extract fastq" version="1.0.0">
  <description> format reads from NCBI SRA.</description>
  <command>fastq-dump --log-level fatal --report never --accession '${input.name}' --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>
  <stdio>
    <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
  </stdio>
  <requirements>
    <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
  </requirements>
  <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>