<tool id="sam_dump" name="Extract reads" version="1.1.1">
  <description> in SAM format from NCBI SRA.</description>
  <command>
    sam-dump --log-level fatal 
    #if str( $region ) != "":
      --aligned-region $region
    #end if
    #if str( $matepairDist ) != "":
      --matepair-distance $matepairDist
    #end if
    #if str( $minMapq ) != "":
      --minmapq $minMapq
    #end if
    #if $header == "yes":
      --header
    #else:
      --no-header 
    #end if
    #if str( $alignments ) == "both":
      --unaligned
    #end if
    #if str( $alignments ) == "unaligned":
      --unaligned-spots-only
    #end if
    #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
      --primary
    #end if
    #if str( $fastq ) == "yes":
      --fastq
    #end if
    #if $input.input_select == "file":
      $input.file
    #elif $input.input_select == "accession_number":
      $input.accession 
    #elif $input.input_select == "text":
      `cat $input.text`
    #end if
    > $output
  </command>  
  <version_string>sam-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>
        <option value="text">text file containing SRR accession</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>
      <when value="text">
        <param format="txt" name="text" type="data" label="text file"/>
      </when>
    </conditional>
    <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="header" type="select" value="yes">
      <label>output SAM header</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="primary" type="select" value="no">
      <label>only primary aligments</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
    <param format="text" name="fastq" type="select" value="no">
      <label>output fastq</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data name="output" format="sam">
      <change_format>
        <when input="fastq" value="yes" format="fastq"/>
      </change_format>
    </data>
  </outputs>
  <requirements>
    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
  </requirements>
  <help>
    This tool extracts reads from sra archives using sam-dump. 
    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
    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 mdshw5@gmail.com for support and bug reports.
  </help>
</tool>