<tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
  <description> from NCBI sra.</description>
  <command>sra-pileup --log-level fatal 
    #if str( $region ) != "":
      --aligned-region $region
    #end if
    #if str( $minMapq ) != "":
      --minmapq $minMapq
    #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>sra-pileup --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="minMapq" type="text" label="minimum mapping quality"/>
  </inputs>
  <outputs>
    <data format="pileup" name="output"/>
  </outputs>
  <requirements>
    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
  </requirements>
  <help>
    This tool produces pileup format from sra archives using sra-pileup. 
    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
    The sra-pileup 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>