annotate emboss_sixpack.xml @ 17:ce385837c160 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"

<tool id="EMBOSS: sixpack90" name="sixpack" version="@VERSION@+galaxy2">
  <!-- tool adds file description and timestamp to output data -->
  <description>Display a DNA sequence with 6-frame translation and ORFs</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command><![CDATA[
    sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize 
    #if str($uppercase):
      -uppercase '$uppercase' 
    #end if  
    -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 name="input1" type="data" format="fasta" label="Sequences" />
    <param name="table" type="select" label="Code to use">
      <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">
      <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">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="mstart" type="select" label="Displays only ORFs starting with an M">
      <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">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
    <param name="uppercase" type="text" value="" label="Regions to put in uppercase" help="If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-alpha-numeric character. Three examples of region specifications are: 1) 24-45, 56-78 2) 1:45, 67=99;765..888 3) 1,5,8,10,23,45,57,99"/>
    <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" />
    <param name="length" type="integer" value="0" label="Line length of page" />
    <param name="margin" type="integer" value="10" label="Margin around sequence for numbering" />
    <param name="disp_name" type="select" label="Display the ID name of the sequence">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="description" type="select" label="Display the description of the sequence">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="offset" type="integer" value="1" label="Number from which you want the DNA sequence to be numbered" />
    <param name="html_out1" type="select" label="Format output as an HTML table">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format2" type="select" label="Output sequence file format">
      <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 name="ofile1" format="sixpack" />
    <data name="ofile2" format="fasta" />
  </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="ofile1" file="emboss_sixpack_out2.sixpack" />
      <output name="ofile2" file="emboss_sixpack_out.fasta"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sixpack.html
  </help>
  <expand macro="citations" />
</tool>