galaxy/tools/emboss_5/emboss_prettyplot.xml

<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
  <!-- produces png output with file name -->
  <description>Displays aligned sequences, with colouring and boxing</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>prettyplot -sequences '$input1' -graph png -goutfile '$out_file1' -residuesperline '$residuesperline' -resbreak '$resbreak' -ccolours '$ccolours' -cidentity '$cidentity' -csimilarity '$csimilarity'
  -cother '$cother' -docolour '$docolour' -gtitle '$title' -pair '$pair' -identity '$identity' -box '$box' -boxcol '$box'col -boxcolval '$box'colval -name '$name' -maxnamelen '$maxnamelen' -number '$number' -listoptions
  '$listoptions' -consensus '$consensus' -collision '$collision' -alternative '$alternative' -showscore '$showscore' -portrait '$portrait' -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="residuesperline" size="10" type="text" value="50">
      <label>The number of residues to be displayed on each line</label>
    </param>
    <param name="resbreak" size="10" type="text" value="50">
      <label>Residues before a space</label>
    </param>
    <param name="ccolours" type="select">
      <label>Colour residues by their consensus value</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="cidentity" size="10" type="text" value="RED">
      <label>Colour to display identical residues</label>
    </param>
    <param name="csimilarity" size="10" type="text" value="GREEN">
      <label>Colour to display similar residues</label>
    </param>
    <param name="cother" size="10" type="text" value="BLACK">
      <label>Colour to display other residues</label>
    </param>
    <param name="docolour" type="select">
      <label>Colour residues by table oily, amide etc.</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="title" type="select">
      <label>Display the title</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="pair" size="10" type="text" value="1.5,1.0,0.5">
      <label>Values to represent identical similar related</label>
    </param>
    <param name="identity" size="10" type="text" value="0">
      <label>Only match those which are identical in all sequences</label>
    </param>
    <param name="box" type="select">
      <label>Display prettyboxes</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="boxcol" type="select">
      <label>Colour the background in the boxes</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="boxcolval" size="10" type="text" value="GREY">
      <label>Colour to be used for background</label>
    </param>
    <param name="name" type="select">
      <label>Display the sequence names</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="maxnamelen" size="10" type="text" value="10">
      <label>Margin size for the sequence name</label>
    </param>
    <param name="number" type="select">
      <label>Display the residue number</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="listoptions" type="select">
      <label>Display the date and options used</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="consensus" type="select">
      <label>Display the consensus</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="collision" type="select">
      <label>Allow collisions in calculating consensus</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="alternative" type="select">
      <label>Use alternative collisions routine</label>
      <option value="0">Normal collision check</option>
      <option value="1">Checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred</option>
      <option value="2">If another residue has a greater than or equal to matching score and these do not match then a collision has occurred</option>
      <option value="3">Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured</option>
    </param>
    <param name="showscore" size="10" type="text" value="-1">
      <label>Print residue scores</label>
    </param>
    <param name="portrait" type="select">
      <label>Set page to Portrait</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="out_file1" />
  </outputs>
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.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>