<tool id="EMBOSS: eprimer3" name="eprimer3" version="5.0.0">
  <description>Picks PCR primers and hybridization oligos and convert it to tabular</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="python">
      eprimer3.py 
          -sequence $input1 
          -outfile $out_file1
          -numreturn $numreturn
          -gcclamp $gcclamp
          -osize $osize
          -minsize $minsize
          -maxsize $maxsize
          -otm $otm
          -mintm $mintm
          -maxtm $maxtm
          -maxdifftm $maxdifftm
          -ogcpercent $ogcpercent
          -mingc $mingc
          -maxgc $maxgc
          -saltconc $saltconc
          -dnaconc $dnaconc
          $hybridprobe
  </command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="hybridprobe" label="Hybrid probe" help="An internal oligo is intended to be used as a hybridization probe" type="boolean" truevalue="-hybridprobe" falsevalue="" checked="False" />
    <param name="numreturn" label="Number of results" help="Maximum number of primer pairs to return" type="integer" value="5"/>
    <param name="gcclamp" label="GC clamp" help="Number of consecutive Gs and Cs at 3' end of both the forward and reverse primer" type="integer" value="0"/>
    <param name="osize" label="Optimum size" help="Optimum length of a primer oligo" type="integer" value="20"/>
    <param name="minsize" label="Min size" help="Minimum acceptable length of a primer" type="integer" value="18"/>
    <param name="maxsize" label="Max size" help="Maximum acceptable length of a primer" type="integer" value="27"/>
    <param name="otm" label="Optimum tm" help="Optimum melting tempreture" type="float" value="60.0"/>
    <param name="mintm" label="Minimum tm" help="Minimum melting tempreture" type="float" value="57.0"/>
    <param name="maxtm" label="Maximum tm" help="Maximum melting tempreture" type="float" value="63.0"/>
    <param name="maxdifftm" label="Maximum difftm" help="Maximum acceptable difference between the melting tempertures of the forward and reverse primers" type="float" value="100.0"/>
    <param name="ogcpercent" label="Optimum GC%" help="Primer optimum GC percent" type="float" value="50.0"/>
    <param name="mingc" label="Minimum GC%" help="Minimum allowable GC percent" type="float" value="20.0"/>
    <param name="maxgc" label="Maximum GC%" help="Maximum allowable GC percent" type="float" value="80.0"/>
    <param name="saltconc" label="Salt concentration" help="The millimolar concentration of salt in the PCR." type="float" value="50.0"/>
    <param name="dnaconc" label="DNA concentration" help="Nanomolar concentration of annealing oligos in the PCR" type="float" value="50.0"/>
    <param name="maxpolyx" label="Maximum allowable polyx" help="Maximum allowable length of a mononucleotide repeat in a primer, for example AAAAA" type="integer" value="5"/>
    <param name="productsize" label="Optimum product size" help="Optimum size for the PCR product. 0 indicates that there is no optimum product size" type="integer" value="200"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <output name="out_file1" file="emboss_revseq_out.fasta"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/eprimer3.html
  </help>
</tool>
