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comparison emboss_prettyplot.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0"> 1 <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0.1">
2 <!-- produces png output with file name --> 2 <!-- produces png output with file name -->
3 <description>Displays aligned sequences, with colouring and boxing</description> 3 <description>Displays aligned sequences, with colouring and boxing</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity 5 <import>macros.xml</import>
6 -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions 6 </macros>
7 <expand macro="requirements" />
8 <command>prettyplot -sequences '$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
7 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> 10 $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
8 <inputs> 11 <inputs>
9 <param format="data" name="input1" type="data"> 12 <param name="input1" type="data" format="data" label="Sequence" />
10 <label>Sequence</label> 13 <param name="residuesperline" type="integer" value="50" label="The number of residues to be displayed on each line" />
11 </param> 14 <param name="resbreak" type="integer" value="50" label="Residues before a space" />
12 <param name="residuesperline" type="text" value="50"> 15 <param name="ccolours" type="select" label="Colour residues by their consensus value">
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> 16 <option value="yes">Yes</option>
21 <option value="no">No</option> 17 <option value="no">No</option>
22 </param> 18 </param>
23 <param name="cidentity" type="text" value="RED"> 19 <param name="cidentity" type="text" value="RED" label="Colour to display identical residues" />
24 <label>Colour to display identical residues</label> 20 <param name="csimilarity" type="text" value="GREEN" label="Colour to display similar residues" />
25 </param> 21 <param name="cother" type="text" value="BLACK" label="Colour to display other residues" />
26 <param name="csimilarity" type="text" value="GREEN"> 22 <param name="docolour" type="select" label="Colour residues by table oily, amide etc.">
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> 23 <option value="no">No</option>
35 <option value="yes">Yes</option> 24 <option value="yes">Yes</option>
36 </param> 25 </param>
37 <param name="title" type="select"> 26 <param name="title" type="select" label="Display the title">
38 <label>Display the title</label>
39 <option value="yes">Yes</option> 27 <option value="yes">Yes</option>
40 <option value="no">No</option> 28 <option value="no">No</option>
41 </param> 29 </param>
42 <param name="pair" type="text" value="1.5,1.0,0.5"> 30 <param name="pair" type="text" value="1.5,1.0,0.5" label="Values to represent identical similar related" />
43 <label>Values to represent identical similar related</label> 31 <param name="identity" type="integer" value="0" label="Only match those which are identical in all sequences" />
44 </param> 32 <param name="box" type="select" label="Display prettyboxes">
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> 33 <option value="yes">Yes</option>
51 <option value="no">No</option> 34 <option value="no">No</option>
52 </param> 35 </param>
53 <param name="boxcol" type="select"> 36 <param name="boxcol" type="select" label="Colour the background in the boxes">
54 <label>Colour the background in the boxes</label>
55 <option value="no">No</option> 37 <option value="no">No</option>
56 <option value="yes">Yes</option> 38 <option value="yes">Yes</option>
57 </param> 39 </param>
58 <param name="boxcolval" type="text" value="GREY"> 40 <param name="boxcolval" type="text" value="GREY" label="Colour to be used for background" />
59 <label>Colour to be used for background</label> 41 <param name="name" type="select" label="Display the sequence names">
60 </param>
61 <param name="name" type="select">
62 <label>Display the sequence names</label>
63 <option value="yes">Yes</option> 42 <option value="yes">Yes</option>
64 <option value="no">No</option> 43 <option value="no">No</option>
65 </param> 44 </param>
66 <param name="maxnamelen" type="text" value="10"> 45 <param name="maxnamelen" type="integer" value="10" label="Margin size for the sequence name" />
67 <label>Margin size for the sequence name</label> 46 <param name="number" type="select" label="Display the residue number">
68 </param>
69 <param name="number" type="select">
70 <label>Display the residue number</label>
71 <option value="yes">Yes</option> 47 <option value="yes">Yes</option>
72 <option value="no">No</option> 48 <option value="no">No</option>
73 </param> 49 </param>
74 <param name="listoptions" type="select"> 50 <param name="listoptions" type="select" label="Display the date and options used">
75 <label>Display the date and options used</label>
76 <option value="yes">Yes</option> 51 <option value="yes">Yes</option>
77 <option value="no">No</option> 52 <option value="no">No</option>
78 </param> 53 </param>
79 <param name="consensus" type="select"> 54 <param name="consensus" type="select" label="Display the consensus">
80 <label>Display the consensus</label>
81 <option value="no">No</option> 55 <option value="no">No</option>
82 <option value="yes">Yes</option> 56 <option value="yes">Yes</option>
83 </param> 57 </param>
84 <param name="collision" type="select"> 58 <param name="collision" type="select" label="Allow collisions in calculating consensus">
85 <label>Allow collisions in calculating consensus</label>
86 <option value="yes">Yes</option> 59 <option value="yes">Yes</option>
87 <option value="no">No</option> 60 <option value="no">No</option>
88 </param> 61 </param>
89 <param name="alternative" type="select"> 62 <param name="alternative" type="select" label="Use alternative collisions routine">
90 <label>Use alternative collisions routine</label>
91 <option value="0">Normal collision check</option> 63 <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> 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>
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> 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>
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> 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>
95 </param> 67 </param>
96 <param name="showscore" type="text" value="-1"> 68 <param name="showscore" type="integer" value="-1" label="Print residue scores" />
97 <label>Print residue scores</label> 69 <param name="portrait" type="select" label="Set page to Portrait">
98 </param>
99 <param name="portrait" type="select">
100 <label>Set page to Portrait</label>
101 <option value="no">No</option> 70 <option value="no">No</option>
102 <option value="yes">Yes</option> 71 <option value="yes">Yes</option>
103 </param> 72 </param>
104 </inputs> 73 </inputs>
105 <outputs> 74 <outputs>
106 <data format="png" name="out_file1" /> 75 <data name="out_file1" format="png" />
107 </outputs> 76 </outputs>
108 <help> 77 <help>
109 You can view the original documentation here_. 78 You can view the original documentation here_.
110
111 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html
112 79
113 ------ 80 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyplot.html
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> 81 </help>
82 <expand macro="citations" />
121 </tool> 83 </tool>