Mercurial > repos > devteam > emboss_5

annotate 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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children 0e2484b6829b
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10
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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" 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" 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" 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" 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" 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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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38 <label>Display the title</label>
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39 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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40 <option value="no">No</option>
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41 </param>
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42 <param name="pair" 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" type="text" value="0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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54 <label>Colour the background in the boxes</label>
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55 <option value="no">No</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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56 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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57 </param>
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58 <param name="boxcolval" 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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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62 <label>Display the sequence names</label>
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63 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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64 <option value="no">No</option>
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65 </param>
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66 <param name="maxnamelen" type="text" value="10">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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70 <label>Display the residue number</label>
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71 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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75 <label>Display the date and options used</label>
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76 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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" 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
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113 ------
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114
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115 **Citation**
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116
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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;`_
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118
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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;`_
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120 </help>
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121 </tool>