<tool id="fastq_dump" name="Extract reads" version="1.1.1">
  <description> from NCBI SRA.</description>
  <command>
    fastq-dump --log-level fatal
    #if $input.input_select == "file":
      --accession '${input.file.name}'
    #else:
      --accession $input.accession
    #end if
    --defline-seq '@\$sn[_\$rn]/\$ri'
    --stdout
    #if $split == "yes":
      --split-spot
    #end if
    #if str( $alignments ) == "aligned":
      --aligned
    #end if
    #if str( $alignments ) == "unaligned":
      --unaligned
    #end if
    #if str( $minID ) != "":
      --minSpotId $minID
    #end if
    #if str( $maxID ) != "":
      --maxSpotId $maxID
    #end if
    #if str( $minlen ) != "":
      --minReadLen $minlen
    #end if
    #if str( $readfilter ) != "":
      --read-filter $readfilter
    #end if
    #if str( $region ) != "":
      --aligned-region $region
    #end if
    #if str( $spotgroups ) != "":
      --spot-groups $spotgroups
    #end if
    #if str( $matepairDist ) != "":
      --matepair-distance $matepairDist
    #end if
    #if $clip == "yes":
      --clip
    #end if
    #if str( $outputformat ) == "fasta":
      --fasta
    #end if
    #if $input.input_select=="file":
      $input.file
    #else:
        $input.accession
    #end if
    > $output
  </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="minID" type="text" label="minimum spot ID"/>
    <param format="text" name="maxID" type="text" label="maximum spot ID"/>
    <param format="text" name="minlen" type="text" label="minimum read length"/>
    <param format="text" name="split" type="select" value="yes">
      <label>split spot by read pairs</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param format="text" name="alignments" type="select" value="both">
      <label>aligned or unaligned reads</label>
      <option value="both">both</option>
      <option value="aligned">aligned only</option>
        <option value="unaligned">unaligned only</option>
    </param>
    <param format="text" name="region" type="text" label="aligned region"/>
    <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
    <param format="text" name="readfilter" type="select" value="">
      <label>filter by value</label>
      <option value="">None</option>
      <option value="pass">pass</option>
      <option value="reject">reject</option>
      <option value="criteria">criteria</option>
      <option value="redacted">redacted</option>
    </param>
    <param name="outputformat" type="select" label="select output format">
      <option value="fastqsanger">fastq</option>
      <option value="fasta">fasta</option>
    </param>
    <param format="text" name="spotgroups" type="text" label="filter by spot-groups"/>
    <param format="text" name="clip" type="select" value="no">
      <label>apply left and right clips</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="fastq" name="output">
        <change_format>
            <when input="outputformat" value="fasta" format="fasta" />
        </change_format>
    </data>
  </outputs>
  <stdio>
    <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
  </stdio>
  <requirements>
    <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
  </requirements>
  <help>
    This tool extracts reads from SRA archives using fastq-dump.
    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
    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 mdshw5@gmail.com for support and bug reports.
  </help>
</tool>