view emboss_sixpack.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba

<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0">
  <!-- tool adds file description and timestamp to output data -->
  <description>Display a DNA sequence with 6-frame translation and ORFs</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
  "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="table" type="select">
      <label>Code to use</label>
      <option value="0">Standard</option>
      <option value="1">Standard (with alternative initiation codons)</option>
      <option value="2">Vertebrate Mitochondrial</option>
      <option value="3">Yeast Mitochondrial</option>
      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
      <option value="5">Invertebrate Mitochondrial</option>
      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
      <option value="9">Echinoderm Mitochondrial</option>
      <option value="10">Euplotid Nuclear</option>
      <option value="11">Bacterial</option>
      <option value="12">Alternative Yeast Nuclear</option>
      <option value="13">Ascidian Mitochondrial</option>
      <option value="14">Flatworm Mitochondrial</option>
      <option value="15">Blepharisma Macronuclear</option>
      <option value="16">Chlorophycean Mitochondrial</option>
      <option value="21">Trematode Mitochondrial</option>
      <option value="22">Scenedesmus obliquus</option>
      <option value="23">Thraustochytrium Mitochondrial</option>
    </param>
    <param name="firstorf" type="select">
      <label>Count the beginning of a sequence as a possible ORF</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="lastorf" type="select">
      <label>Count the end of a sequence as a possible ORF</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="mstart" type="select">
      <label>Displays only ORFs starting with an M</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="reverse" type="select">
      <label>Display the translation of the DNA sequence in the 3 reverse frames</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="orfminsize" type="text" value="1">
      <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label>
    </param>
    <param name="uppercase" type="text" value="">
      <label>Regions to put in uppercase</label>
    </param>
    <param name="number" type="select">
      <label>Number the sequence at the beginning and the end of each line</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="width" type="text" value="60">
      <label>Number of nucleotides displayed on each line</label>
    </param>
    <param name="length" type="text" value="0">
      <label>Line length of page</label>
    </param>
    <param name="margin" type="text" value="10">
      <label>Margin around sequence for numbering</label>
    </param>
    <param name="disp_name" type="select">
      <label>Display the ID name of the sequence</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="description" type="select">
      <label>Display the description of the sequence</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="offset" type="text" value="1">
      <label>Number from which you want the DNA sequence to be numbered</label>
    </param>
    <param name="html_out1" type="select">
      <label>Format output as an HTML table</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format2" type="select">
      <label>Output Sequence File Format</label>
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>
      <option value="embl">EMBL (m)</option>
      <option value="fitch">Fitch (m)</option>
      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
      <option value="genbank">GENBANK (m)</option>
      <option value="gff">GFF (m)</option>
      <option value="hennig86">Hennig86 (m)</option>
      <option value="ig">Intelligenetics (m)</option>
      <option value="jackknifer">Jackknifer (m)</option>
      <option value="jackknifernon">Jackknifernon (m)</option>
      <option value="mega">Mega (m)</option>
      <option value="meganon">Meganon (m)</option>
      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
      <option value="pir">NBRF (PIR) (m)</option>
      <option value="ncbi">NCBI style FASTA (m)</option>
      <option value="nexus">Nexus/PAUP (m)</option>
      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
      <option value="phylip">PHYLIP interleaved (m)</option>
      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
      <option value="selex">SELEX (m)</option>
      <option value="staden">Staden (s)</option>
      <option value="strider">DNA strider (m)</option>
      <option value="swiss">SwisProt entry (m)</option>
      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data format="sixpack" name="ofile1" />
    <data format="fasta" name="ofile2" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="table" value="0"/>
      <param name="firstorf" value="no"/>
      <param name="lastorf" value="no"/>
      <param name="mstart" value="no"/>
      <param name="reverse" value="no"/>
      <param name="orfminsize" value="1"/>
      <param name="uppercase" value=""/>
      <param name="number" value="no"/>
      <param name="width" value="60"/>
      <param name="length" value="0"/>
      <param name="margin" value="10"/>
      <param name="disp_name" value="no"/>
      <param name="description" value="no"/>
      <param name="offset" value="1"/>
      <param name="html_out1" value="no"/>
      <param name="out_format2" value="fasta"/>
      <output name="ofile2" file="emboss_sixpack_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/sixpack.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>