Mercurial > repos > devteam > emboss_5
comparison emboss_5/emboss_prettyplot.xml @ 8:b810c96613ee draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:12:41 -0500 |
| parents | b94ca591877b |
| children |
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| 7:ce22ceec214a | 8:b810c96613ee |
|---|---|
| 7 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> | 7 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> |
| 8 <inputs> | 8 <inputs> |
| 9 <param format="data" name="input1" type="data"> | 9 <param format="data" name="input1" type="data"> |
| 10 <label>Sequence</label> | 10 <label>Sequence</label> |
| 11 </param> | 11 </param> |
| 12 <param name="residuesperline" size="10" type="text" value="50"> | 12 <param name="residuesperline" type="text" value="50"> |
| 13 <label>The number of residues to be displayed on each line</label> | 13 <label>The number of residues to be displayed on each line</label> |
| 14 </param> | 14 </param> |
| 15 <param name="resbreak" size="10" type="text" value="50"> | 15 <param name="resbreak" type="text" value="50"> |
| 16 <label>Residues before a space</label> | 16 <label>Residues before a space</label> |
| 17 </param> | 17 </param> |
| 18 <param name="ccolours" type="select"> | 18 <param name="ccolours" type="select"> |
| 19 <label>Colour residues by their consensus value</label> | 19 <label>Colour residues by their consensus value</label> |
| 20 <option value="yes">Yes</option> | 20 <option value="yes">Yes</option> |
| 21 <option value="no">No</option> | 21 <option value="no">No</option> |
| 22 </param> | 22 </param> |
| 23 <param name="cidentity" size="10" type="text" value="RED"> | 23 <param name="cidentity" type="text" value="RED"> |
| 24 <label>Colour to display identical residues</label> | 24 <label>Colour to display identical residues</label> |
| 25 </param> | 25 </param> |
| 26 <param name="csimilarity" size="10" type="text" value="GREEN"> | 26 <param name="csimilarity" type="text" value="GREEN"> |
| 27 <label>Colour to display similar residues</label> | 27 <label>Colour to display similar residues</label> |
| 28 </param> | 28 </param> |
| 29 <param name="cother" size="10" type="text" value="BLACK"> | 29 <param name="cother" type="text" value="BLACK"> |
| 30 <label>Colour to display other residues</label> | 30 <label>Colour to display other residues</label> |
| 31 </param> | 31 </param> |
| 32 <param name="docolour" type="select"> | 32 <param name="docolour" type="select"> |
| 33 <label>Colour residues by table oily, amide etc.</label> | 33 <label>Colour residues by table oily, amide etc.</label> |
| 34 <option value="no">No</option> | 34 <option value="no">No</option> |
| 37 <param name="title" type="select"> | 37 <param name="title" type="select"> |
| 38 <label>Display the title</label> | 38 <label>Display the title</label> |
| 39 <option value="yes">Yes</option> | 39 <option value="yes">Yes</option> |
| 40 <option value="no">No</option> | 40 <option value="no">No</option> |
| 41 </param> | 41 </param> |
| 42 <param name="pair" size="10" type="text" value="1.5,1.0,0.5"> | 42 <param name="pair" type="text" value="1.5,1.0,0.5"> |
| 43 <label>Values to represent identical similar related</label> | 43 <label>Values to represent identical similar related</label> |
| 44 </param> | 44 </param> |
| 45 <param name="identity" size="10" type="text" value="0"> | 45 <param name="identity" type="text" value="0"> |
| 46 <label>Only match those which are identical in all sequences</label> | 46 <label>Only match those which are identical in all sequences</label> |
| 47 </param> | 47 </param> |
| 48 <param name="box" type="select"> | 48 <param name="box" type="select"> |
| 49 <label>Display prettyboxes</label> | 49 <label>Display prettyboxes</label> |
| 50 <option value="yes">Yes</option> | 50 <option value="yes">Yes</option> |
| 53 <param name="boxcol" type="select"> | 53 <param name="boxcol" type="select"> |
| 54 <label>Colour the background in the boxes</label> | 54 <label>Colour the background in the boxes</label> |
| 55 <option value="no">No</option> | 55 <option value="no">No</option> |
| 56 <option value="yes">Yes</option> | 56 <option value="yes">Yes</option> |
| 57 </param> | 57 </param> |
| 58 <param name="boxcolval" size="10" type="text" value="GREY"> | 58 <param name="boxcolval" type="text" value="GREY"> |
| 59 <label>Colour to be used for background</label> | 59 <label>Colour to be used for background</label> |
| 60 </param> | 60 </param> |
| 61 <param name="name" type="select"> | 61 <param name="name" type="select"> |
| 62 <label>Display the sequence names</label> | 62 <label>Display the sequence names</label> |
| 63 <option value="yes">Yes</option> | 63 <option value="yes">Yes</option> |
| 64 <option value="no">No</option> | 64 <option value="no">No</option> |
| 65 </param> | 65 </param> |
| 66 <param name="maxnamelen" size="10" type="text" value="10"> | 66 <param name="maxnamelen" type="text" value="10"> |
| 67 <label>Margin size for the sequence name</label> | 67 <label>Margin size for the sequence name</label> |
| 68 </param> | 68 </param> |
| 69 <param name="number" type="select"> | 69 <param name="number" type="select"> |
| 70 <label>Display the residue number</label> | 70 <label>Display the residue number</label> |
| 71 <option value="yes">Yes</option> | 71 <option value="yes">Yes</option> |
| 91 <option value="0">Normal collision check</option> | 91 <option value="0">Normal collision check</option> |
| 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> | 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> |
| 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> | 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> |
| 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> | 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> |
| 95 </param> | 95 </param> |
| 96 <param name="showscore" size="10" type="text" value="-1"> | 96 <param name="showscore" type="text" value="-1"> |
| 97 <label>Print residue scores</label> | 97 <label>Print residue scores</label> |
| 98 </param> | 98 </param> |
| 99 <param name="portrait" type="select"> | 99 <param name="portrait" type="select"> |
| 100 <label>Set page to Portrait</label> | 100 <label>Set page to Portrait</label> |
| 101 <option value="no">No</option> | 101 <option value="no">No</option> |