[2] | 1 | <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
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| 2 | <!-- produces png output with file name --> |
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| 3 | <description>Displays aligned sequences, with colouring and boxing</description>
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| 4 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 5 | <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
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| 6 | -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
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| 7 | $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
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| 8 | <inputs>
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| 9 | <param format="data" name="input1" type="data">
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| 10 | <label>Sequence</label>
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| 11 | </param>
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| 12 | <param name="residuesperline" size="10" type="text" value="50">
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| 13 | <label>The number of residues to be displayed on each line</label>
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| 14 | </param>
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| 15 | <param name="resbreak" size="10" type="text" value="50">
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| 16 | <label>Residues before a space</label>
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| 17 | </param>
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| 18 | <param name="ccolours" type="select">
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| 19 | <label>Colour residues by their consensus value</label>
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| 20 | <option value="yes">Yes</option>
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| 21 | <option value="no">No</option>
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| 22 | </param>
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| 23 | <param name="cidentity" size="10" type="text" value="RED">
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| 24 | <label>Colour to display identical residues</label>
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| 25 | </param>
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| 26 | <param name="csimilarity" size="10" type="text" value="GREEN">
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| 27 | <label>Colour to display similar residues</label>
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| 28 | </param>
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| 29 | <param name="cother" size="10" type="text" value="BLACK">
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| 30 | <label>Colour to display other residues</label>
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| 31 | </param>
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| 32 | <param name="docolour" type="select">
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| 33 | <label>Colour residues by table oily, amide etc.</label>
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| 34 | <option value="no">No</option>
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| 35 | <option value="yes">Yes</option>
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| 36 | </param>
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| 37 | <param name="title" type="select">
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| 38 | <label>Display the title</label>
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| 39 | <option value="yes">Yes</option>
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| 40 | <option value="no">No</option>
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| 41 | </param>
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| 42 | <param name="pair" size="10" type="text" value="1.5,1.0,0.5">
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| 43 | <label>Values to represent identical similar related</label>
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| 44 | </param>
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| 45 | <param name="identity" size="10" type="text" value="0">
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| 46 | <label>Only match those which are identical in all sequences</label>
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| 47 | </param>
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| 48 | <param name="box" type="select">
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| 49 | <label>Display prettyboxes</label>
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| 50 | <option value="yes">Yes</option>
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| 51 | <option value="no">No</option>
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| 52 | </param>
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| 53 | <param name="boxcol" type="select">
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| 54 | <label>Colour the background in the boxes</label>
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| 55 | <option value="no">No</option>
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| 56 | <option value="yes">Yes</option>
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| 57 | </param>
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| 58 | <param name="boxcolval" size="10" type="text" value="GREY">
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| 59 | <label>Colour to be used for background</label>
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| 60 | </param>
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| 61 | <param name="name" type="select">
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| 62 | <label>Display the sequence names</label>
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| 63 | <option value="yes">Yes</option>
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| 64 | <option value="no">No</option>
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| 65 | </param>
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| 66 | <param name="maxnamelen" size="10" type="text" value="10">
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| 67 | <label>Margin size for the sequence name</label>
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| 68 | </param>
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| 69 | <param name="number" type="select">
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| 70 | <label>Display the residue number</label>
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| 71 | <option value="yes">Yes</option>
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| 72 | <option value="no">No</option>
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| 73 | </param>
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| 74 | <param name="listoptions" type="select">
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| 75 | <label>Display the date and options used</label>
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| 76 | <option value="yes">Yes</option>
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| 77 | <option value="no">No</option>
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| 78 | </param>
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| 79 | <param name="consensus" type="select">
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| 80 | <label>Display the consensus</label>
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| 81 | <option value="no">No</option>
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| 82 | <option value="yes">Yes</option>
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| 83 | </param>
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| 84 | <param name="collision" type="select">
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| 85 | <label>Allow collisions in calculating consensus</label>
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| 86 | <option value="yes">Yes</option>
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| 87 | <option value="no">No</option>
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| 88 | </param>
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| 89 | <param name="alternative" type="select">
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| 90 | <label>Use alternative collisions routine</label>
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| 91 | <option value="0">Normal collision check</option>
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| 92 | <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>
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| 93 | <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>
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| 94 | <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>
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| 95 | </param>
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| 96 | <param name="showscore" size="10" type="text" value="-1">
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| 97 | <label>Print residue scores</label>
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| 98 | </param>
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| 99 | <param name="portrait" type="select">
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| 100 | <label>Set page to Portrait</label>
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| 101 | <option value="no">No</option>
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| 102 | <option value="yes">Yes</option>
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| 103 | </param>
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| 104 | </inputs>
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| 105 | <outputs>
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| 106 | <data format="png" name="out_file1" />
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| 107 | </outputs>
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| 108 | <help> |
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| 109 | You can view the original documentation here_. |
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| 110 | |
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| 111 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html |
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| 112 | </help> |
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| 113 | </tool> |
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