view fastq_dump.xml @ 29:d5f7232e67d9 draft

debug prefetch caching and accession input for fastq_dump

<tool id="fastq_dump" name="Extract fastq" version="1.0.3">
  <description> format reads from NCBI sra.</description>
  <command>
    #if $input.input_select=="file"
        fastq-dump --log-level fatal --accession '${input.sra.name}' --stdout $split $aligned $input.file > $output 
    #else
        fastq-dump --log-level fatal --accession $input.accession --stdout $split $aligned $input.accession > $output 
    #end if
  </command>
  <version_string>fastq-dump --version</version_string>
  <inputs>
    <conditional name="input">
      <param name="input_select" type="select" label="Select input type">
        <option value="accession_number">SRR accession</option>
        <option value="file">SRA archive in current history</option>
      </param>
      <when value="file">
	<param format="sra" name="file" type="data" label="sra archive"/>
      </when>
      <when value="accession_number">
	<param format="text" name="accession" type="text" label="accession"/>
      </when>
    </conditional>
    <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 fastq format 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.
    Contact Matt Shirley at [e-mail] for support and bug reports.
  </help>
</tool>