Mercurial > repos > devteam > emboss_5
comparison emboss_prettyplot.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
| author | iuc |
|---|---|
| date | Wed, 08 Feb 2017 12:42:22 -0500 |
| parents | |
| children | 8992d258e42f |
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| 9:511429456d3c | 10:d49956b87f7e |
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| 1 <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0.1"> | |
| 2 <!-- produces png output with file name --> | |
| 3 <description>Displays aligned sequences, with colouring and boxing</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <command>prettyplot -sequences '$input1' -graph png -goutfile '$out_file1' -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity '$cidentity' -csimilarity '$csimilarity' | |
| 9 -cother '$cother' -docolour $docolour -gtitle $title -pair '$pair' -identity $identity -box $box -boxcol $boxcol -boxcolval '$boxcolval' -name $name -maxnamelen $maxnamelen -number $number -listoptions | |
| 10 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> | |
| 11 <inputs> | |
| 12 <param name="input1" type="data" format="data" label="Sequence" /> | |
| 13 <param name="residuesperline" type="integer" value="50" label="The number of residues to be displayed on each line" /> | |
| 14 <param name="resbreak" type="integer" value="50" label="Residues before a space" /> | |
| 15 <param name="ccolours" type="select" label="Colour residues by their consensus value"> | |
| 16 <option value="yes">Yes</option> | |
| 17 <option value="no">No</option> | |
| 18 </param> | |
| 19 <param name="cidentity" type="text" value="RED" label="Colour to display identical residues" /> | |
| 20 <param name="csimilarity" type="text" value="GREEN" label="Colour to display similar residues" /> | |
| 21 <param name="cother" type="text" value="BLACK" label="Colour to display other residues" /> | |
| 22 <param name="docolour" type="select" label="Colour residues by table oily, amide etc."> | |
| 23 <option value="no">No</option> | |
| 24 <option value="yes">Yes</option> | |
| 25 </param> | |
| 26 <param name="title" type="select" label="Display the title"> | |
| 27 <option value="yes">Yes</option> | |
| 28 <option value="no">No</option> | |
| 29 </param> | |
| 30 <param name="pair" type="text" value="1.5,1.0,0.5" label="Values to represent identical similar related" /> | |
| 31 <param name="identity" type="integer" value="0" label="Only match those which are identical in all sequences" /> | |
| 32 <param name="box" type="select" label="Display prettyboxes"> | |
| 33 <option value="yes">Yes</option> | |
| 34 <option value="no">No</option> | |
| 35 </param> | |
| 36 <param name="boxcol" type="select" label="Colour the background in the boxes"> | |
| 37 <option value="no">No</option> | |
| 38 <option value="yes">Yes</option> | |
| 39 </param> | |
| 40 <param name="boxcolval" type="text" value="GREY" label="Colour to be used for background" /> | |
| 41 <param name="name" type="select" label="Display the sequence names"> | |
| 42 <option value="yes">Yes</option> | |
| 43 <option value="no">No</option> | |
| 44 </param> | |
| 45 <param name="maxnamelen" type="integer" value="10" label="Margin size for the sequence name" /> | |
| 46 <param name="number" type="select" label="Display the residue number"> | |
| 47 <option value="yes">Yes</option> | |
| 48 <option value="no">No</option> | |
| 49 </param> | |
| 50 <param name="listoptions" type="select" label="Display the date and options used"> | |
| 51 <option value="yes">Yes</option> | |
| 52 <option value="no">No</option> | |
| 53 </param> | |
| 54 <param name="consensus" type="select" label="Display the consensus"> | |
| 55 <option value="no">No</option> | |
| 56 <option value="yes">Yes</option> | |
| 57 </param> | |
| 58 <param name="collision" type="select" label="Allow collisions in calculating consensus"> | |
| 59 <option value="yes">Yes</option> | |
| 60 <option value="no">No</option> | |
| 61 </param> | |
| 62 <param name="alternative" type="select" label="Use alternative collisions routine"> | |
| 63 <option value="0">Normal collision check</option> | |
| 64 <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> | |
| 65 <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> | |
| 66 <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> | |
| 67 </param> | |
| 68 <param name="showscore" type="integer" value="-1" label="Print residue scores" /> | |
| 69 <param name="portrait" type="select" label="Set page to Portrait"> | |
| 70 <option value="no">No</option> | |
| 71 <option value="yes">Yes</option> | |
| 72 </param> | |
| 73 </inputs> | |
| 74 <outputs> | |
| 75 <data name="out_file1" format="png" /> | |
| 76 </outputs> | |
| 77 <help> | |
| 78 You can view the original documentation here_. | |
| 79 | |
| 80 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyplot.html | |
| 81 </help> | |
| 82 <expand macro="citations" /> | |
| 83 </tool> |