comparison emboss_prettyplot.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

10:d49956b87f7e

<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0.1">
  <!-- produces png output with file name -->
  <description>Displays aligned sequences, with colouring and boxing</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="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 $boxcol -boxcolval '$boxcolval' -name $name -maxnamelen $maxnamelen -number $number -listoptions
  $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="residuesperline" type="integer" value="50" label="The number of residues to be displayed on each line" />
    <param name="resbreak" type="integer" value="50" label="Residues before a space" />
    <param name="ccolours" type="select" label="Colour residues by their consensus value">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="cidentity" type="text" value="RED" label="Colour to display identical residues" />
    <param name="csimilarity" type="text" value="GREEN" label="Colour to display similar residues" />
    <param name="cother" type="text" value="BLACK" label="Colour to display other residues" />
    <param name="docolour" type="select" label="Colour residues by table oily, amide etc.">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="title" type="select" label="Display the title">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="pair" type="text" value="1.5,1.0,0.5" label="Values to represent identical similar related" />
    <param name="identity" type="integer" value="0" label="Only match those which are identical in all sequences" />
    <param name="box" type="select" label="Display prettyboxes">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="boxcol" type="select" label="Colour the background in the boxes">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="boxcolval" type="text" value="GREY" label="Colour to be used for background" />
    <param name="name" type="select" label="Display the sequence names">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="maxnamelen" type="integer" value="10" label="Margin size for the sequence name" />
    <param name="number" type="select" label="Display the residue number">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="listoptions" type="select" label="Display the date and options used">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="consensus" type="select" label="Display the consensus">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="collision" type="select" label="Allow collisions in calculating consensus">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="alternative" type="select" label="Use alternative collisions routine">
      <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" type="integer" value="-1" label="Print residue scores" />
    <param name="portrait" type="select" label="Set page to Portrait">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="png" />
  </outputs>
  <help>
    You can view the original documentation here_.

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