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author xuebing
date Sat, 31 Mar 2012 08:53:06 -0400
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<tool id="fastqdump" name="fastq-dump">
  <description>convert SRA to FASTQ</description>
  <command>/Users/xuebing/tools/sratoolkit.2.1.9-mac32/fastq-dump -A $input -M $minReadLen -Z > $out_file1 </command>
  <inputs>
    <param name="input" format="sra" type="data" label="Original file (SRA)"/>
    <param name="minReadLen" size="10" type="integer" value="10" label="minimum read length to output"/>
  </inputs>
  <outputs>
    <data format="fastq" name="out_file1" />
  </outputs>
  <help>

**What it does**

This is a wrapper of the fastq-dump tool from sra-toolkit. See http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software 

  </help>
</tool>