<tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">

  <description>Searches DNA sequences for matches with primer pairs</description>

  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>

  <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>

  <inputs>

    <param format="fasta" name="input1" type="data">

      <label>Main sequences</label>

    </param>

    <param format="data" name="input2" type="data">

      <label>Primer file</label>

    </param>

    <param name="mismatchpercent" size="4" type="text" value="0">

      <label>Allowed percent mismatch</label>

    </param>

  </inputs>

  <outputs>

    <data format="primersearch" name="out_file1" />

  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="emboss_primersearch.fasta"/>
      <param name="mismatchpercent" value="0"/>
      <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
    </test>
  </tests>

  <help>

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html



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**Citation**



If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>