annotate Codonlogo.xml @ 10:20716450be87

Uploaded
author davidmurphy
date Mon, 30 Jan 2012 21:17:50 -0500
parents f3462128e87c
children 981eb8c3a756
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1 <tool id="codonlogo" name="Codon Logo" version="3">
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2 <description>generator for fasta (eg Clustal alignments)</description>
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
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3 <command interpreter="python -W ignore::DeprecationWarning">
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4 codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth
4
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5
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davidmurphy
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6 #if str($ylabel) != ''
8
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7 -x "$xlabel"
4
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8 #end if
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9
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davidmurphy
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10 #if str( $ylabel) != ''
8
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11 -y "$ylabel"
4
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12 #end if
8
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13
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14 #if str($range.mode) == 'part'
4
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davidmurphy
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15 -l "$range.seqstart" -u "$range.seqend"
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16 #end if
8
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davidmurphy
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17 #if str($comp.mode) == 'equiprobable'
4
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davidmurphy
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18 --composition 'equiprobable'
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davidmurphy
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19 #end if
8
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20 #if str($comp.mode) == 'none'
4
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davidmurphy
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21 --composition 'none'
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davidmurphy
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22 #end if
8
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davidmurphy
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23 #if str($comp.mode) == 'file'
4
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davidmurphy
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24 -R $compfile
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davidmurphy
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25 #end if
8
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davidmurphy
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26 #if str($comp.mode) == 'Escherichiacoli'
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
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27 --comp escherichiacoli
8
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28 #end if
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davidmurphy
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29 #if str($comp.mode) == 'Saccharomycescerevisiae'
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
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30 --comp saccharomycescerevisiae
8
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31 #end if
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32 #if str($comp.mode) == 'Homosapiens'
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f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
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33 --comp homosapiens
8
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34 #end if
4
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35
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davidmurphy
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36 #if $colours.colour == 'part'
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37
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davidmurphy
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38 #if str( $colours.colorAAA) != ''
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davidmurphy
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39 -C $colours.colorAAA AAA ""
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davidmurphy
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40 #end if
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41
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davidmurphy
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42 #if str( $colours.colorAAC) != ''
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davidmurphy
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43 -C $colours.colorAAC AAC ""
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davidmurphy
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44 #end if
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45
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davidmurphy
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46 #if str( $colours.colorAAG) != ''
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davidmurphy
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47 -C $colours.colorAAG AAG ""
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davidmurphy
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48 #end if
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49
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davidmurphy
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50 #if str( $colours.colorAAU) != ''
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davidmurphy
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51 -C $colours.colorAAU AAU ""
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davidmurphy
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52 -C $colours.colorAAU AAT ""
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davidmurphy
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53 #end if
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54
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davidmurphy
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55 #if str( $colours.colorACA) != ''
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davidmurphy
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56 -C $colours.colorACA ACA ""
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davidmurphy
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57 #end if
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58
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davidmurphy
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59 #if str( $colours.colorACC) != ''
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davidmurphy
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60 -C $colours.colorACC ACC ""
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davidmurphy
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61 #end if
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62
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davidmurphy
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63 #if str( $colours.colorACG) != ''
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davidmurphy
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64 -C $colours.colorACG ACG ""
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davidmurphy
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65 #end if
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66
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67 #if str( $colours.colorACU) != ''
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davidmurphy
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68 -C $colours.colorACU ACU ""
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davidmurphy
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69 -C $colours.colorACU ACT ""
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davidmurphy
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70 #end if
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71
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davidmurphy
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72 #if str( $colours.colorAGA) != ''
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davidmurphy
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73 -C $colours.colorAGA AGA ""
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davidmurphy
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74 #end if
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75
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davidmurphy
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76 #if str( $colours.colorAGC) != ''
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davidmurphy
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77 -C $colours.colorAGC AGC ""
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davidmurphy
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78 #end if
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79
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davidmurphy
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80 #if str( $colours.colorAGG) != ''
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davidmurphy
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81 -C $colours.colorAGG AGG ""
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davidmurphy
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82 #end if
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83
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davidmurphy
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84 #if str( $colours.colorAGU) != ''
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davidmurphy
parents:
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85 -C $colours.colorAGU AGU ""
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davidmurphy
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86 -C $colours.colorAGU AGT ""
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davidmurphy
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87 #end if
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88
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davidmurphy
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89 #if str( $colours.colorAUA) != ''
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davidmurphy
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90 -C $colours.colorAUA AUA ""
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davidmurphy
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91 -C $colours.colorAUA ATA ""
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davidmurphy
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92 #end if
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93
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94 #if str( $colours.colorAUC) != ''
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davidmurphy
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95 -C $colours.colorAUC AUC ""
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davidmurphy
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96 -C $colours.colorAUC ATC ""
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davidmurphy
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97 #end if
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98
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99 #if str( $colours.colorAUG) != ''
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davidmurphy
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100 -C $colours.colorAUG AUG ""
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davidmurphy
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101 -C $colours.colorAUG ATG ""
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davidmurphy
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102 #end if
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103
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davidmurphy
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104 #if str( $colours.colorAUU) != ''
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davidmurphy
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105 -C $colours.colorAUU AUU ""
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davidmurphy
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106 -C $colours.colorAUU ATT ""
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davidmurphy
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107 #end if
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davidmurphy
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108
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davidmurphy
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109 #if str( $colours.colorCAA) != ''
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davidmurphy
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110 -C $colours.colorCAA CAA ""
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davidmurphy
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111 #end if
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112
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113 #if str( $colours.colorCAC) != ''
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davidmurphy
parents:
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114 -C $colours.colorCAC CAC ""
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davidmurphy
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115 #end if
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davidmurphy
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116
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davidmurphy
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117 #if str( $colours.colorCAG) != ''
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davidmurphy
parents:
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118 -C $colours.colorCAG CAG ""
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davidmurphy
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119 #end if
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davidmurphy
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120
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davidmurphy
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121 #if str( $colours.colorCAU) != ''
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davidmurphy
parents:
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122 -C $colours.colorCAU CAU ""
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davidmurphy
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123 -C $colours.colorCAU CAT ""
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davidmurphy
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124 #end if
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125
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davidmurphy
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126 #if str( $colours.colorCCA) != ''
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davidmurphy
parents:
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127 -C $colours.colorCCA CCA ""
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davidmurphy
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128 #end if
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129
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davidmurphy
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130 #if str( $colours.colorCCC) != ''
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davidmurphy
parents:
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131 -C $colours.colorCCC CCC ""
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davidmurphy
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132 #end if
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133
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davidmurphy
parents:
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134 #if str( $colours.colorCCG) != ''
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davidmurphy
parents:
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135 -C $colours.colorCCG CCG ""
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davidmurphy
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136 #end if
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davidmurphy
parents:
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137
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davidmurphy
parents:
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138 #if str( $colours.colorCCU) != ''
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davidmurphy
parents:
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139 -C $colours.colorCCU CCU ""
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davidmurphy
parents:
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140 -C $colours.colorCCU CCT ""
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davidmurphy
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141 #end if
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davidmurphy
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142
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davidmurphy
parents:
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143 #if str( $colours.colorCGA) != ''
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davidmurphy
parents:
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144 -C $colours.colorCGA CGA ""
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davidmurphy
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145 #end if
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parents:
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146
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davidmurphy
parents:
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147 #if str( $colours.colorCGC) != ''
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davidmurphy
parents:
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148 -C $colours.colorCGC CGC ""
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davidmurphy
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149 #end if
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davidmurphy
parents:
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150
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davidmurphy
parents:
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151 #if str( $colours.colorCGG) != ''
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davidmurphy
parents:
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152 -C $colours.colorCGG CGG ""
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davidmurphy
parents:
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153 #end if
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davidmurphy
parents:
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154
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davidmurphy
parents:
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155 #if str( $colours.colorCGU) != ''
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davidmurphy
parents:
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156 -C $colours.colorCGU CGU ""
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davidmurphy
parents:
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157 -C $colours.colorCGU CGT ""
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davidmurphy
parents:
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158 #end if
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davidmurphy
parents:
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159
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davidmurphy
parents:
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160 #if str( $colours.colorCUA) != ''
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davidmurphy
parents:
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161 -C $colours.colorCUA CUA ""
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davidmurphy
parents:
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162 -C $colours.colorCUA CTA ""
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davidmurphy
parents:
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163 #end if
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davidmurphy
parents:
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164
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davidmurphy
parents:
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165 #if str( $colours.colorCUC) != ''
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davidmurphy
parents:
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166 -C $colours.colorCUC CUC ""
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davidmurphy
parents:
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167 -C $colours.colorCUC CTC ""
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davidmurphy
parents:
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168 #end if
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davidmurphy
parents:
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169
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davidmurphy
parents:
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170 #if str( $colours.colorCUG) != ''
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davidmurphy
parents:
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171 -C $colours.colorCUG CUG ""
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davidmurphy
parents:
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172 -C $colours.colorCUG CTG ""
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davidmurphy
parents:
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173 #end if
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davidmurphy
parents:
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174
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davidmurphy
parents:
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175 #if str( $colours.colorCUU) != ''
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davidmurphy
parents:
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176 -C $colours.colorCUU CUU ""
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davidmurphy
parents:
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177 -C $colours.colorCUU CTT ""
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davidmurphy
parents:
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178 #end if
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davidmurphy
parents:
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179
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davidmurphy
parents:
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180 #if str( $colours.colorGAA) != ''
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davidmurphy
parents:
diff changeset
181 -C $colours.colorGAA GAA ""
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davidmurphy
parents:
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182 #end if
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davidmurphy
parents:
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183
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davidmurphy
parents:
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184 #if str( $colours.colorGAC) != ''
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davidmurphy
parents:
diff changeset
185 -C $colours.colorGAC GAC ""
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davidmurphy
parents:
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186 #end if
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davidmurphy
parents:
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187
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davidmurphy
parents:
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188 #if str( $colours.colorGAG) != ''
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davidmurphy
parents:
diff changeset
189 -C $colours.colorGAG GAG ""
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davidmurphy
parents:
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190 #end if
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davidmurphy
parents:
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191
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davidmurphy
parents:
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192 #if str( $colours.colorGAU) != ''
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davidmurphy
parents:
diff changeset
193 -C $colours.colorGAU GAU ""
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davidmurphy
parents:
diff changeset
194 -C $colours.colorGAU GAT ""
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davidmurphy
parents:
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195 #end if
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davidmurphy
parents:
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196
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davidmurphy
parents:
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197 #if str( $colours.colorGCA) != ''
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davidmurphy
parents:
diff changeset
198 -C $colours.colorGCA GCA ""
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davidmurphy
parents:
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199 #end if
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davidmurphy
parents:
diff changeset
200
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
201 #if str( $colours.colorGCC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
202 -C $colours.colorGCC GCC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
203 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
204
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
205 #if str( $colours.colorGCG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
206 -C $colours.colorGCG GCG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
207 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
208
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
209 #if str( $colours.colorGCU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
210 -C $colours.colorGCU GCU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
211 -C $colours.colorGCU GCT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
212 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
213
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
214 #if str( $colours.colorGGA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
215 -C $colours.colorGGA GGA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
216 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
217
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
218 #if str( $colours.colorGGC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
219 -C $colours.colorGGC GGC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
220 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
221
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
222 #if str( $colours.colorGGG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
223 -C $colours.colorGGG GGG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
224 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
225
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
226 #if str( $colours.colorGGU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
227 -C $colours.colorGGU GGU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
228 -C $colours.colorGGU GGT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
229 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
230
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
231 #if str( $colours.colorGUA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
232 -C $colours.colorGUA GUA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
233 -C $colours.colorGUA GTA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
234 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
235
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
236 #if str( $colours.colorGUC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
237 -C $colours.colorGUC GUC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
238 -C $colours.colorGUC GTC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
239 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
240
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
241 #if str( $colours.colorGUG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
242 -C $colours.colorGUG GUG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
243 -C $colours.colorGUG GTG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
244 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
245
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
246 #if str( $colours.colorGUU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
247 -C $colours.colorGUU GUU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
248 -C $colours.colorGUU GTT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
249 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
250
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
251 #if str( $colours.colorUAA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
252 -C $colours.colorUAA UAA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
253 -C $colours.colorUAA TAA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
254 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
255
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
256 #if str( $colours.colorUAC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
257 -C $colours.colorUAC UAC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
258 -C $colours.colorUAC TAC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
259 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
260
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
261 #if str( $colours.colorUAG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
262 -C $colours.colorUAG UAG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
263 -C $colours.colorUAG TAG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
264 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
265
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
266 #if str( $colours.colorUAU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
267 -C $colours.colorUAU UAU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
268 -C $colours.colorUAU TAT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
269 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
270
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
271 #if str( $colours.colorUCA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
272 -C $colours.colorUCA UCA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
273 -C $colours.colorUCA TCA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
274 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
275
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
276 #if str( $colours.colorUCC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
277 -C $colours.colorUCC UCC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
278 -C $colours.colorUCC TCC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
279 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
280
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
281 #if str( $colours.colorUCG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
282 -C $colours.colorUCG UCG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
283 -C $colours.colorUCG TCG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
284 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
285
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
286 #if str( $colours.colorUCU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
287 -C $colours.colorUCU UCU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
288 -C $colours.colorUCU TCT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
289 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
290
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
291 #if str( $colours.colorUGA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
292 -C $colours.colorUGA UGA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
293 -C $colours.colorUGA TGA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
294 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
295
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
296 #if str( $colours.colorUGC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
297 -C $colours.colorUGC UGC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
298 -C $colours.colorUGC TGC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
299 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
300
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
301 #if str( $colours.colorUGG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
302 -C $colours.colorUGG UGG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
303 -C $colours.colorUGG TGG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
304 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
305
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
306 #if str( $colours.colorUGU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
307 -C $colours.colorUGU UGU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
308 -C $colours.colorUGU TGT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
309 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
310
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
311 #if str( $colours.colorUUA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
312 -C $colours.colorUUA UUA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
313 -C $colours.colorUUA TTA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
314 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
315
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
316 #if str( $colours.colorUUC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
317 -C $colours.colorUUC UUC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
318 -C $colours.colorUUC TTC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
319 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
320
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
321 #if str( $colours.colorUUG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
322 -C $colours.colorUUG UUG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
323 -C $colours.colorUUG TTG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
324 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
325
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
326 #if str( $colours.colorUUU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
327 -C $colours.colorUUU UUU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
328 -C $colours.colorUUU TTT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
329 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
330 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
331
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
332 </command>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
333 <inputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
334 <page>
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
335 <param format="text" name="input" type="data" label="Input file.(must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon)" />
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
336
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
337 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
338
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
339 <param name="outformat" type="select" label="Output format for image (or text report)" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
340 <option value="png" selected="True">PNG screen quality</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
341 <option value="png_print">High quality printable PNG</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
342 <option value="pdf">PDF</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
343 <option value="jpeg">JPG</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
344 <option value="eps">EPS</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
345 <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
346 </param>
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
347 <param name="resolution" size="5" type="integer" value="96" label="Bitmap resolution in dots per inch (DPI).For high quality printable PNG this should be set to 600" />
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
348
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
349 <param name="frame" type="select" label="Frame to view the alignment. If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
350 <option value="0" selected="True">0</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
351 <option value="1">+1</option>
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
352 <option value="2">+2</option>
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
353 <option value="3">reverse complement 0</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
354 <option value="4">reverse complement +1</option>
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
355 <option value="5">reverse complement +2</option>
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
356 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
357 <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
358 <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
359 <option value="True" selected="True">Yes</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
360 <option value="False">No</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
361 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
362 <param name="xlabel" label="X-axis label" type="text" size="50" value="" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
363 <param name="ylabel" label="Y-axis label" type="text" size="50" value="" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
364
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
365 <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.1" />
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
366
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
367 <param name="stackwidth" size="5" type="float" value="40.0" label="Width of a logo stack" />
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
368
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
369 <param name="stackheight" size="5" type="integer" value="100" label="height of a logo stack" />
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
370 <param name="box" type="select" display="radio" label="Draw boxes around symbols?" >
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
371 <option value="True" >Yes</option>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
372 <option value="False" selected="True">No</option>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
373 </param>
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
374 <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
375 <option value="True" selected="True">Yes</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
376 <option value="False">No</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
377 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
378 <param name="errorbars" type="select" display="radio" label="Display error bars?" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
379 <option value="True" selected="True">Yes</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
380 <option value="False">No</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
381 </param>
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
382 <param name="scalewidth" type="select" display="radio" label="Scale the visible stack width by the fraction of symbols in the column?" >
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
383 <option value="True" selected="True">Yes</option>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
384 <option value="False">No</option>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
385 </param>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
386 <param name="strict" type="select" display="radio" label="Allow gaps which are not in groups of 3/ allow codons with ambiguous nucleotides." >
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
387 <option value="False" selected="True">Yes</option>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
388 <option value="True" >No</option>
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
389 </param>
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
390 <conditional name="range">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
391 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
392 <option value="complete" selected="true">complete sequence</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
393 <option value="part">Only use a part of the sequence</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
394 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
395 <when value="complete">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
396 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
397 <when value="part">
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
398 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying codon numbers outside the sequence lengths will cause unpredictable but bad consequences!"
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
399 label="Index_start (eg 1=first codon) of the start of the sequence range to include in the logo">
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
400 </param>
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
401 <param name="seqend" size="5" type="integer" value="99999" label="Index_end (eg 75=75th codon) of the end of the sequence range to include in the logo" >
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
402 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
403 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
404 </conditional>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
405 <conditional name="comp">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
406 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file">
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
407 <option value="none" >No small sample correction</option>
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
408 <option value="equiprobable" >Equiprobable</option>
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
409 <option value="Homosapiens" >Human</option>
10
20716450be87 Uploaded
davidmurphy
parents: 9
diff changeset
410 <option value="Saccharomycescerevisiae" >Yeast</option>
20716450be87 Uploaded
davidmurphy
parents: 9
diff changeset
411 <option value="Escherichiacoli" >E.Coli</option>
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
412 <option value="From File">from file</option>
4
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
413
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
414 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
415 <when value="auto">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
416 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
417 <when value="equiprobable">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
418 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
419 <when value="none">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
420 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
421 <when value="file">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
422 <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weigt." />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
423 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
424
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
425 </conditional>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
426 <conditional name="colours">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
427 <param name="colour" type="select" label="Choose colours?(it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc. )">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
428 <option value="no" selected="true">Default colours</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
429 <option value="part">Set your own.</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
430 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
431 <when value="no">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
432 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
433 <when value="part">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
434
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
435 <param name="colorAAA" size="10" type="text" value="" label="AAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
436 <param name="colorAAC" size="10" type="text" value="" label="AAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
437 <param name="colorAAG" size="10" type="text" value="" label="AAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
438 <param name="colorAAU" size="10" type="text" value="" label="AAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
439 <param name="colorACA" size="10" type="text" value="" label="ACA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
440 <param name="colorACC" size="10" type="text" value="" label="ACC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
441 <param name="colorACG" size="10" type="text" value="" label="ACG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
442 <param name="colorACU" size="10" type="text" value="" label="ACU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
443 <param name="colorAGA" size="10" type="text" value="" label="AGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
444 <param name="colorAGC" size="10" type="text" value="" label="AGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
445 <param name="colorAGG" size="10" type="text" value="" label="AGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
446 <param name="colorAGU" size="10" type="text" value="" label="AGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
447 <param name="colorAUA" size="10" type="text" value="" label="AUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
448 <param name="colorAUC" size="10" type="text" value="" label="AUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
449 <param name="colorAUG" size="10" type="text" value="" label="AUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
450 <param name="colorAUU" size="10" type="text" value="" label="AUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
451 <param name="colorCAA" size="10" type="text" value="" label="CAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
452 <param name="colorCAC" size="10" type="text" value="" label="CAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
453 <param name="colorCAG" size="10" type="text" value="" label="CAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
454 <param name="colorCAU" size="10" type="text" value="" label="CAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
455 <param name="colorCCA" size="10" type="text" value="" label="CCA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
456 <param name="colorCCC" size="10" type="text" value="" label="CCC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
457 <param name="colorCCG" size="10" type="text" value="" label="CCG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
458 <param name="colorCCU" size="10" type="text" value="" label="CCU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
459 <param name="colorCGA" size="10" type="text" value="" label="CGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
460 <param name="colorCGC" size="10" type="text" value="" label="CGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
461 <param name="colorCGG" size="10" type="text" value="" label="CGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
462 <param name="colorCGU" size="10" type="text" value="" label="CGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
463 <param name="colorCUA" size="10" type="text" value="" label="CUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
464 <param name="colorCUC" size="10" type="text" value="" label="CUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
465 <param name="colorCUG" size="10" type="text" value="" label="CUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
466 <param name="colorCUU" size="10" type="text" value="" label="CUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
467 <param name="colorGAA" size="10" type="text" value="" label="GAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
468 <param name="colorGAC" size="10" type="text" value="" label="GAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
469 <param name="colorGAG" size="10" type="text" value="" label="GAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
470 <param name="colorGAU" size="10" type="text" value="" label="GAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
471 <param name="colorGCA" size="10" type="text" value="" label="GCA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
472 <param name="colorGCC" size="10" type="text" value="" label="GCC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
473 <param name="colorGCG" size="10" type="text" value="" label="GCG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
474 <param name="colorGCU" size="10" type="text" value="" label="GCU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
475 <param name="colorGGA" size="10" type="text" value="" label="GGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
476 <param name="colorGGC" size="10" type="text" value="" label="GGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
477 <param name="colorGGG" size="10" type="text" value="" label="GGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
478 <param name="colorGGU" size="10" type="text" value="" label="GGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
479 <param name="colorGUA" size="10" type="text" value="" label="GUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
480 <param name="colorGUC" size="10" type="text" value="" label="GUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
481 <param name="colorGUG" size="10" type="text" value="" label="GUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
482 <param name="colorGUU" size="10" type="text" value="" label="GUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
483 <param name="colorUAA" size="10" type="text" value="" label="UAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
484 <param name="colorUAC" size="10" type="text" value="" label="UAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
485 <param name="colorUAG" size="10" type="text" value="" label="UAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
486 <param name="colorUAU" size="10" type="text" value="" label="UAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
487 <param name="colorUCA" size="10" type="text" value="" label="UCA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
488 <param name="colorUCC" size="10" type="text" value="" label="UCC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
489 <param name="colorUCG" size="10" type="text" value="" label="UCG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
490 <param name="colorUCU" size="10" type="text" value="" label="UCU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
491 <param name="colorUGA" size="10" type="text" value="" label="UGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
492 <param name="colorUGC" size="10" type="text" value="" label="UGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
493 <param name="colorUGG" size="10" type="text" value="" label="UGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
494 <param name="colorUGU" size="10" type="text" value="" label="UGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
495 <param name="colorUUA" size="10" type="text" value="" label="UUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
496 <param name="colorUUC" size="10" type="text" value="" label="UUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
497 <param name="colorUUG" size="10" type="text" value="" label="UUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
498 <param name="colorUUU" size="10" type="text" value="" label="UUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
499
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
500
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
501
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
502 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
503
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
504 </conditional>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
505 <param name="size" type="select" label="Output CodonLogo size" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
506 <option value="large" selected="True">Large</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
507 <option value="medium">Medium</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
508 <option value="small">Small</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
509 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
510
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
511 </page>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
512 </inputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
513 <outputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
514 <data format="pdf" name="output" label="${logoname}_output.${outformat}">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
515 <change_format>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
516 <when input="outformat" value="png_print" format="png" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
517 <when input="outformat" value="png" format="png" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
518 <when input="outformat" value="jpeg" format="jpg" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
519 <when input="outformat" value="eps" format="eps" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
520 <when input="outformat" value="txt" format="txt" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
521 </change_format>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
522 </data>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
523 </outputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
524 <help>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
525
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
526 **Note**
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
527
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
528 This tool uses CodonLogo in Galaxy to generate a sequence logo from a provided alignment.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
529 The input file must be an alignment in your current history.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
530 The tool will attempt to read a provided file and if it is unable to it will generate an error.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
531
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
532 A typical output looks like this
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
533
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
534 .. image:: ./static/images/CodonLogoExample.png
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
535
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
536 ----
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
537
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
538 **Warning about input files**
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
539
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
540 The program used by this tool will fail if your alignment files are not all the same length.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
541
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
542 Fasta alignments from ClustalW Galaxy tool will work but many other fasta files may cause this tool to produce an error and fail - please do not file
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
543 a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
544 sequences are the same length!
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
545
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
546 Files must first be converted to fasta format in order to be used with this tool.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
547
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
548 ----
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
549
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
550 The default colour scheme is based on associated amino acid types:
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
551
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
552 Polar positive
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
553 H, K, R -Light Blue
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
554
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
555 Polar negative
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
556 D, E -Red
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
557
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
558 Polar neutral
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
559 S, T, N, Q -Green
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
560
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
561 Non-polar aliphatic
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
562 A, V, L, I, M -Blue
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
563
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
564 Non-polar aromatic
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
565 F, W, Y -Magenta
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
566 P, G -Brown
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
567 C -Yellow
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
568
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
569 Stop codons -Black
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davidmurphy
parents:
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570
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571
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davidmurphy
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572 **Attribution**
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573
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574
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575 This Galaxy wrapper was modified for CodonLogo by David Murphy and is based on the wrapper written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_
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576
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577 .. _Weblogo3: http://weblogo.berkeley.edu/
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578 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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579 .. _CodonLogo: http://recode.ucc.ie/CodonLogo
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580
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davidmurphy
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581 </help>
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davidmurphy
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582
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davidmurphy
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583 </tool>
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584
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585