annotate emboss_5/emboss_transeq.xml @ 5:2cf967772a40

Fix for emboss_format_corrector.py. Datatypes should be changed before the job is run.

<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
  <description>Translate nucleic acid sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="frame" type="select">
      <label>Frame(s) to translate</label>
      <option value="1">Frame 1</option>
      <option value="2">Frame 2</option>
      <option value="3">Frame 3</option>
      <option value="F">Forward three frames</option>
      <option value="-1">Frame -1</option>
      <option value="-2">Frame -2</option>
      <option value="-3">Frame -3</option>
      <option value="R">Reverse three frames</option>
      <option value="6">All six frames</option>
    </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="regions" size="10" type="text" value="">
      <label>Regions to translate</label>
    </param>
    <param name="trim" type="select">
      <label>Remove all 'X' and '*' characters from the right end of the translation</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="clean" type="select">
      <label>Change all STOP codon positions from the '*' character to 'X'</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="alternative" type="select">
      <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" 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="fasta" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="frame" value="1"/>
      <param name="table" value="0"/>
      <param name="regions" value=""/>
      <param name="trim" value="no"/>
      <param name="clean" value="no"/>
      <param name="alternative" value="no"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_transeq_out.fasta"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark

The input dataset needs to be sequences.

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