view emboss_5/emboss_einverted.xml @ 8:b810c96613ee draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
  <description>Finds DNA inverted repeats</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>On query</label>
    </param>
    <param name="gap" type="text" value="12">
      <label>Gap penalty</label>
    </param>
    <param name="threshold" type="text" value="50">
      <label>Minimum score threshold</label>
    </param>
    <param name="match" type="text" value="3">
      <label>Match score</label>
    </param>
    <param name="mismatch" type="text" value="-4">
      <label>Mismatch score</label>
    </param>
    <param name="maxrepeat" type="text" value="2000">
      <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
    </param>
  </inputs>
  <outputs>
    <data format="einverted" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="gap" value="12"/>
      <param name="threshold" value="50"/>
      <param name="match" value="3"/>
      <param name="mismatch" value="-4"/>
      <param name="maxrepeat" value="2000"/>
      <output name="out_file1" file="emboss_einverted_out.einverted"/>
    </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/einverted.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

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>