<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="2.4.5">sra_toolkit</requirement>
  </requirements>
  <tests>
    <test>
      <param name="input_select" value="accession_number"/>
      <param name="accession" value="SRR925743"/>
      <param name="region" value="17:41243452-41277500"/>
      <output name="output" file="sra_pileup_result.pileup" ftype="pileup" />
    </test>
  </tests>
  <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://github.com/ncbi/sra-tools
      Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy.
  </help>
</tool>