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comparison emboss_prettyplot.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
2 <!-- produces png output with file name -->
3 <description>Displays aligned sequences, with colouring and boxing</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5 <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
6 -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
7 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
8 <inputs>
9 <param format="data" name="input1" type="data">
10 <label>Sequence</label>
11 </param>
12 <param name="residuesperline" type="text" value="50">
13 <label>The number of residues to be displayed on each line</label>
14 </param>
15 <param name="resbreak" type="text" value="50">
16 <label>Residues before a space</label>
17 </param>
18 <param name="ccolours" type="select">
19 <label>Colour residues by their consensus value</label>
20 <option value="yes">Yes</option>
21 <option value="no">No</option>
22 </param>
23 <param name="cidentity" type="text" value="RED">
24 <label>Colour to display identical residues</label>
25 </param>
26 <param name="csimilarity" type="text" value="GREEN">
27 <label>Colour to display similar residues</label>
28 </param>
29 <param name="cother" type="text" value="BLACK">
30 <label>Colour to display other residues</label>
31 </param>
32 <param name="docolour" type="select">
33 <label>Colour residues by table oily, amide etc.</label>
34 <option value="no">No</option>
35 <option value="yes">Yes</option>
36 </param>
37 <param name="title" type="select">
38 <label>Display the title</label>
39 <option value="yes">Yes</option>
40 <option value="no">No</option>
41 </param>
42 <param name="pair" type="text" value="1.5,1.0,0.5">
43 <label>Values to represent identical similar related</label>
44 </param>
45 <param name="identity" type="text" value="0">
46 <label>Only match those which are identical in all sequences</label>
47 </param>
48 <param name="box" type="select">
49 <label>Display prettyboxes</label>
50 <option value="yes">Yes</option>
51 <option value="no">No</option>
52 </param>
53 <param name="boxcol" type="select">
54 <label>Colour the background in the boxes</label>
55 <option value="no">No</option>
56 <option value="yes">Yes</option>
57 </param>
58 <param name="boxcolval" type="text" value="GREY">
59 <label>Colour to be used for background</label>
60 </param>
61 <param name="name" type="select">
62 <label>Display the sequence names</label>
63 <option value="yes">Yes</option>
64 <option value="no">No</option>
65 </param>
66 <param name="maxnamelen" type="text" value="10">
67 <label>Margin size for the sequence name</label>
68 </param>
69 <param name="number" type="select">
70 <label>Display the residue number</label>
71 <option value="yes">Yes</option>
72 <option value="no">No</option>
73 </param>
74 <param name="listoptions" type="select">
75 <label>Display the date and options used</label>
76 <option value="yes">Yes</option>
77 <option value="no">No</option>
78 </param>
79 <param name="consensus" type="select">
80 <label>Display the consensus</label>
81 <option value="no">No</option>
82 <option value="yes">Yes</option>
83 </param>
84 <param name="collision" type="select">
85 <label>Allow collisions in calculating consensus</label>
86 <option value="yes">Yes</option>
87 <option value="no">No</option>
88 </param>
89 <param name="alternative" type="select">
90 <label>Use alternative collisions routine</label>
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>
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>
95 </param>
96 <param name="showscore" type="text" value="-1">
97 <label>Print residue scores</label>
98 </param>
99 <param name="portrait" type="select">
100 <label>Set page to Portrait</label>
101 <option value="no">No</option>
102 <option value="yes">Yes</option>
103 </param>
104 </inputs>
105 <outputs>
106 <data format="png" name="out_file1" />
107 </outputs>
108 <help>
109 You can view the original documentation here_.
110
111 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html
112
113 ------
114
115 **Citation**
116
117 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;`_
118
119 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;`_
120 </help>
121 </tool>