<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
  <description>Align EST and genomic DNA sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
  $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>EST sequence(s)</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>Genomic sequence</label>
    </param>
    <param name="match" size="4" type="text" value="1">
      <label>Score for matching two bases</label>
    </param>
    <param name="mismatch" size="4" type="text" value="1">
      <label>Cost for mismatching two bases</label>
    </param>
    <param name="gappenalty" size="4" type="text" value="2">
      <label>Cost for deleting a single base in either sequence, excluding introns</label>
    </param>
    <param name="intronpenalty" size="4" type="text" value="40">
      <label>Cost for an intron, independent of length</label>
    </param>
    <param name="splicepenalty" size="4" type="text" value="20">
      <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
    </param>
    <param name="minscore" size="4" type="text" value="30">
      <label>Exclude alignments with scores below this threshold score</label>
    </param>
    <param name="reverse" type="select">
      <label>Reverse the orientation of the EST sequence</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="splice" type="select">
      <label>Use donor and acceptor splice sites</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="mode" type="select">
      <label>Comparison mode</label>
      <option value="both">Both strands</option>
      <option value="forward">Forward strand only</option>
      <option value="reverse">Reverse strand only</option>
    </param>
    <param name="best" type="select">
      <label>Only best comparisons</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="shuffle" size="4" type="text" value="0">
      <label>Shuffle</label>
    </param>
    <param name="seed" size="4" type="text" value="20825">
      <label>Random number seed</label>
    </param>
    <param name="align" type="select">
      <label>Show the alignment</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="width" size="4" type="text" value="50">
      <label>Alignment width</label>
    </param>
  </inputs>
  <outputs>
    <data format="est2genome" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="match" value="1"/>
      <param name="mismatch" value="1"/>
      <param name="match" value="1"/>
      <param name="gappenalty" value="2"/>
      <param name="intronpenalty" value="40"/>
      <param name="splicepenalty" value="20"/>
      <param name="minscore" value="30"/>
      <param name="reverse" value="no"/>
      <param name="splice" value="yes"/>
      <param name="mode" value="both"/>
      <param name="best" value="yes"/>
      <param name="shuffle" value="0"/>
      <param name="seed" value="20825"/>
      <param name="align" value="no"/>
      <param name="width" value="50"/>
      <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
    </test>
  </tests>
  <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/est2genome.html
  </help>
</tool>