annotate Codonlogo.xml @ 7:8d676bbd1f2d

Uploaded
author davidmurphy
date Mon, 16 Jan 2012 07:03:36 -0500
parents 4d47ab2b7bcc
children 5149eb3a89c2
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4
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davidmurphy
parents:
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1 <tool id="codonlogo" name="Codon Logo" version="3">
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davidmurphy
parents:
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2 <description>generator for fasta (eg Clustal alignments)</description>
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davidmurphy
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3 <command interpreter="python -W ignore::DeprecationWarning">
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davidmurphy
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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 $errorbars
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davidmurphy
parents:
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5
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davidmurphy
parents:
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6 #if str($ylabel) != ''
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davidmurphy
parents:
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7 -x $xlabel
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davidmurphy
parents:
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8 #end if
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davidmurphy
parents:
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9
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davidmurphy
parents:
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10 #if str( $ylabel) != ''
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davidmurphy
parents:
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11 -y $ylabel
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davidmurphy
parents:
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12 #end if
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davidmurphy
parents:
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13 #if $range.mode == 'part'
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davidmurphy
parents:
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14 -l "$range.seqstart" -u "$range.seqend"
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davidmurphy
parents:
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15 #end if
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davidmurphy
parents:
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16 #if $comp.mode == 'equiprobable'
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davidmurphy
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17 --composition 'equiprobable'
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davidmurphy
parents:
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18 #end if
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davidmurphy
parents:
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19 #if $comp.mode == 'none'
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davidmurphy
parents:
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20 --composition 'none'
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davidmurphy
parents:
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21 #end if
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davidmurphy
parents:
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22 #if $comp.mode == 'file'
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davidmurphy
parents:
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23 -R $compfile
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davidmurphy
parents:
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24 #end if
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davidmurphy
parents:
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25
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davidmurphy
parents:
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26 #if $colours.colour == 'part'
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davidmurphy
parents:
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27
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davidmurphy
parents:
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28 #if str( $colours.colorAAA) != ''
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davidmurphy
parents:
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29 -C $colours.colorAAA AAA ""
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davidmurphy
parents:
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30 #end if
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davidmurphy
parents:
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31
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davidmurphy
parents:
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32 #if str( $colours.colorAAC) != ''
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davidmurphy
parents:
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33 -C $colours.colorAAC AAC ""
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davidmurphy
parents:
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34 #end if
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davidmurphy
parents:
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35
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davidmurphy
parents:
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36 #if str( $colours.colorAAG) != ''
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davidmurphy
parents:
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37 -C $colours.colorAAG AAG ""
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davidmurphy
parents:
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38 #end if
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davidmurphy
parents:
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39
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davidmurphy
parents:
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40 #if str( $colours.colorAAU) != ''
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davidmurphy
parents:
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41 -C $colours.colorAAU AAU ""
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davidmurphy
parents:
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42 -C $colours.colorAAU AAT ""
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davidmurphy
parents:
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43 #end if
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davidmurphy
parents:
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44
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davidmurphy
parents:
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45 #if str( $colours.colorACA) != ''
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davidmurphy
parents:
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46 -C $colours.colorACA ACA ""
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davidmurphy
parents:
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47 #end if
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davidmurphy
parents:
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48
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davidmurphy
parents:
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49 #if str( $colours.colorACC) != ''
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davidmurphy
parents:
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50 -C $colours.colorACC ACC ""
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davidmurphy
parents:
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51 #end if
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davidmurphy
parents:
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52
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davidmurphy
parents:
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53 #if str( $colours.colorACG) != ''
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davidmurphy
parents:
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54 -C $colours.colorACG ACG ""
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davidmurphy
parents:
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55 #end if
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davidmurphy
parents:
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56
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davidmurphy
parents:
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57 #if str( $colours.colorACU) != ''
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davidmurphy
parents:
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58 -C $colours.colorACU ACU ""
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davidmurphy
parents:
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59 -C $colours.colorACU ACT ""
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davidmurphy
parents:
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60 #end if
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davidmurphy
parents:
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61
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davidmurphy
parents:
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62 #if str( $colours.colorAGA) != ''
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davidmurphy
parents:
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63 -C $colours.colorAGA AGA ""
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davidmurphy
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64 #end if
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davidmurphy
parents:
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65
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davidmurphy
parents:
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66 #if str( $colours.colorAGC) != ''
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davidmurphy
parents:
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67 -C $colours.colorAGC AGC ""
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davidmurphy
parents:
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68 #end if
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davidmurphy
parents:
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69
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davidmurphy
parents:
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70 #if str( $colours.colorAGG) != ''
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davidmurphy
parents:
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71 -C $colours.colorAGG AGG ""
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davidmurphy
parents:
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72 #end if
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davidmurphy
parents:
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73
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davidmurphy
parents:
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74 #if str( $colours.colorAGU) != ''
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davidmurphy
parents:
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75 -C $colours.colorAGU AGU ""
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davidmurphy
parents:
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76 -C $colours.colorAGU AGT ""
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davidmurphy
parents:
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77 #end if
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davidmurphy
parents:
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78
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davidmurphy
parents:
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79 #if str( $colours.colorAUA) != ''
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davidmurphy
parents:
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80 -C $colours.colorAUA AUA ""
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davidmurphy
parents:
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81 -C $colours.colorAUA ATA ""
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davidmurphy
parents:
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82 #end if
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davidmurphy
parents:
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83
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davidmurphy
parents:
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84 #if str( $colours.colorAUC) != ''
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davidmurphy
parents:
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85 -C $colours.colorAUC AUC ""
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davidmurphy
parents:
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86 -C $colours.colorAUC ATC ""
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davidmurphy
parents:
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87 #end if
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davidmurphy
parents:
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88
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davidmurphy
parents:
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89 #if str( $colours.colorAUG) != ''
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davidmurphy
parents:
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90 -C $colours.colorAUG AUG ""
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davidmurphy
parents:
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91 -C $colours.colorAUG ATG ""
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davidmurphy
parents:
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92 #end if
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davidmurphy
parents:
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93
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davidmurphy
parents:
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94 #if str( $colours.colorAUU) != ''
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davidmurphy
parents:
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95 -C $colours.colorAUU AUU ""
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davidmurphy
parents:
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96 -C $colours.colorAUU ATT ""
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davidmurphy
parents:
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97 #end if
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davidmurphy
parents:
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98
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davidmurphy
parents:
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99 #if str( $colours.colorCAA) != ''
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davidmurphy
parents:
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100 -C $colours.colorCAA CAA ""
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davidmurphy
parents:
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101 #end if
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davidmurphy
parents:
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102
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davidmurphy
parents:
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103 #if str( $colours.colorCAC) != ''
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davidmurphy
parents:
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104 -C $colours.colorCAC CAC ""
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davidmurphy
parents:
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105 #end if
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davidmurphy
parents:
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106
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davidmurphy
parents:
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107 #if str( $colours.colorCAG) != ''
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davidmurphy
parents:
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108 -C $colours.colorCAG CAG ""
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davidmurphy
parents:
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109 #end if
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davidmurphy
parents:
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110
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davidmurphy
parents:
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111 #if str( $colours.colorCAU) != ''
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davidmurphy
parents:
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112 -C $colours.colorCAU CAU ""
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davidmurphy
parents:
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113 -C $colours.colorCAU CAT ""
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davidmurphy
parents:
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114 #end if
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davidmurphy
parents:
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115
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davidmurphy
parents:
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116 #if str( $colours.colorCCA) != ''
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davidmurphy
parents:
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117 -C $colours.colorCCA CCA ""
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davidmurphy
parents:
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118 #end if
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davidmurphy
parents:
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119
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davidmurphy
parents:
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120 #if str( $colours.colorCCC) != ''
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davidmurphy
parents:
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121 -C $colours.colorCCC CCC ""
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davidmurphy
parents:
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122 #end if
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davidmurphy
parents:
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123
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davidmurphy
parents:
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124 #if str( $colours.colorCCG) != ''
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davidmurphy
parents:
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125 -C $colours.colorCCG CCG ""
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davidmurphy
parents:
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126 #end if
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davidmurphy
parents:
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127
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davidmurphy
parents:
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128 #if str( $colours.colorCCU) != ''
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davidmurphy
parents:
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129 -C $colours.colorCCU CCU ""
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davidmurphy
parents:
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130 -C $colours.colorCCU CCT ""
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davidmurphy
parents:
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131 #end if
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davidmurphy
parents:
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132
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davidmurphy
parents:
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133 #if str( $colours.colorCGA) != ''
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davidmurphy
parents:
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134 -C $colours.colorCGA CGA ""
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davidmurphy
parents:
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135 #end if
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davidmurphy
parents:
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136
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davidmurphy
parents:
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137 #if str( $colours.colorCGC) != ''
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davidmurphy
parents:
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138 -C $colours.colorCGC CGC ""
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davidmurphy
parents:
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139 #end if
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davidmurphy
parents:
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140
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davidmurphy
parents:
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141 #if str( $colours.colorCGG) != ''
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davidmurphy
parents:
diff changeset
142 -C $colours.colorCGG CGG ""
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davidmurphy
parents:
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143 #end if
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davidmurphy
parents:
diff changeset
144
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davidmurphy
parents:
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145 #if str( $colours.colorCGU) != ''
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davidmurphy
parents:
diff changeset
146 -C $colours.colorCGU CGU ""
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davidmurphy
parents:
diff changeset
147 -C $colours.colorCGU CGT ""
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davidmurphy
parents:
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148 #end if
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davidmurphy
parents:
diff changeset
149
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davidmurphy
parents:
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150 #if str( $colours.colorCUA) != ''
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davidmurphy
parents:
diff changeset
151 -C $colours.colorCUA CUA ""
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davidmurphy
parents:
diff changeset
152 -C $colours.colorCUA CTA ""
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davidmurphy
parents:
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153 #end if
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davidmurphy
parents:
diff changeset
154
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davidmurphy
parents:
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155 #if str( $colours.colorCUC) != ''
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davidmurphy
parents:
diff changeset
156 -C $colours.colorCUC CUC ""
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davidmurphy
parents:
diff changeset
157 -C $colours.colorCUC CTC ""
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davidmurphy
parents:
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158 #end if
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davidmurphy
parents:
diff changeset
159
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davidmurphy
parents:
diff changeset
160 #if str( $colours.colorCUG) != ''
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davidmurphy
parents:
diff changeset
161 -C $colours.colorCUG CUG ""
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davidmurphy
parents:
diff changeset
162 -C $colours.colorCUG CTG ""
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davidmurphy
parents:
diff changeset
163 #end if
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davidmurphy
parents:
diff changeset
164
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davidmurphy
parents:
diff changeset
165 #if str( $colours.colorCUU) != ''
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davidmurphy
parents:
diff changeset
166 -C $colours.colorCUU CUU ""
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davidmurphy
parents:
diff changeset
167 -C $colours.colorCUU CTT ""
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davidmurphy
parents:
diff changeset
168 #end if
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davidmurphy
parents:
diff changeset
169
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davidmurphy
parents:
diff changeset
170 #if str( $colours.colorGAA) != ''
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davidmurphy
parents:
diff changeset
171 -C $colours.colorGAA GAA ""
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davidmurphy
parents:
diff changeset
172 #end if
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davidmurphy
parents:
diff changeset
173
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davidmurphy
parents:
diff changeset
174 #if str( $colours.colorGAC) != ''
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davidmurphy
parents:
diff changeset
175 -C $colours.colorGAC GAC ""
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davidmurphy
parents:
diff changeset
176 #end if
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davidmurphy
parents:
diff changeset
177
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davidmurphy
parents:
diff changeset
178 #if str( $colours.colorGAG) != ''
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davidmurphy
parents:
diff changeset
179 -C $colours.colorGAG GAG ""
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davidmurphy
parents:
diff changeset
180 #end if
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davidmurphy
parents:
diff changeset
181
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davidmurphy
parents:
diff changeset
182 #if str( $colours.colorGAU) != ''
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davidmurphy
parents:
diff changeset
183 -C $colours.colorGAU GAU ""
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davidmurphy
parents:
diff changeset
184 -C $colours.colorGAU GAT ""
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davidmurphy
parents:
diff changeset
185 #end if
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davidmurphy
parents:
diff changeset
186
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davidmurphy
parents:
diff changeset
187 #if str( $colours.colorGCA) != ''
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davidmurphy
parents:
diff changeset
188 -C $colours.colorGCA GCA ""
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davidmurphy
parents:
diff changeset
189 #end if
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davidmurphy
parents:
diff changeset
190
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davidmurphy
parents:
diff changeset
191 #if str( $colours.colorGCC) != ''
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davidmurphy
parents:
diff changeset
192 -C $colours.colorGCC GCC ""
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davidmurphy
parents:
diff changeset
193 #end if
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davidmurphy
parents:
diff changeset
194
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davidmurphy
parents:
diff changeset
195 #if str( $colours.colorGCG) != ''
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davidmurphy
parents:
diff changeset
196 -C $colours.colorGCG GCG ""
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davidmurphy
parents:
diff changeset
197 #end if
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davidmurphy
parents:
diff changeset
198
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davidmurphy
parents:
diff changeset
199 #if str( $colours.colorGCU) != ''
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davidmurphy
parents:
diff changeset
200 -C $colours.colorGCU GCU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
201 -C $colours.colorGCU GCT ""
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davidmurphy
parents:
diff changeset
202 #end if
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davidmurphy
parents:
diff changeset
203
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davidmurphy
parents:
diff changeset
204 #if str( $colours.colorGGA) != ''
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davidmurphy
parents:
diff changeset
205 -C $colours.colorGGA GGA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
206 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
207
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
208 #if str( $colours.colorGGC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
209 -C $colours.colorGGC GGC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
210 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
211
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
212 #if str( $colours.colorGGG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
213 -C $colours.colorGGG GGG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
214 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
215
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
216 #if str( $colours.colorGGU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
217 -C $colours.colorGGU GGU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
218 -C $colours.colorGGU GGT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
219 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
220
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
221 #if str( $colours.colorGUA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
222 -C $colours.colorGUA GUA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
223 -C $colours.colorGUA GTA ""
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.colorGUC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
227 -C $colours.colorGUC GUC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
228 -C $colours.colorGUC GTC ""
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.colorGUG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
232 -C $colours.colorGUG GUG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
233 -C $colours.colorGUG GTG ""
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.colorGUU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
237 -C $colours.colorGUU GUU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
238 -C $colours.colorGUU GTT ""
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.colorUAA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
242 -C $colours.colorUAA UAA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
243 -C $colours.colorUAA TAA ""
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.colorUAC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
247 -C $colours.colorUAC UAC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
248 -C $colours.colorUAC TAC ""
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.colorUAG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
252 -C $colours.colorUAG UAG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
253 -C $colours.colorUAG TAG ""
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.colorUAU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
257 -C $colours.colorUAU UAU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
258 -C $colours.colorUAU TAT ""
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.colorUCA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
262 -C $colours.colorUCA UCA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
263 -C $colours.colorUCA TCA ""
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.colorUCC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
267 -C $colours.colorUCC UCC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
268 -C $colours.colorUCC TCC ""
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.colorUCG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
272 -C $colours.colorUCG UCG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
273 -C $colours.colorUCG TCG ""
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.colorUCU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
277 -C $colours.colorUCU UCU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
278 -C $colours.colorUCU TCT ""
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.colorUGA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
282 -C $colours.colorUGA UGA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
283 -C $colours.colorUGA TGA ""
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.colorUGC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
287 -C $colours.colorUGC UGC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
288 -C $colours.colorUGC TGC ""
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.colorUGG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
292 -C $colours.colorUGG UGG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
293 -C $colours.colorUGG TGG ""
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.colorUGU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
297 -C $colours.colorUGU UGU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
298 -C $colours.colorUGU TGT ""
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.colorUUA) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
302 -C $colours.colorUUA UUA ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
303 -C $colours.colorUUA TTA ""
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.colorUUC) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
307 -C $colours.colorUUC UUC ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
308 -C $colours.colorUUC TTC ""
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.colorUUG) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
312 -C $colours.colorUUG UUG ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
313 -C $colours.colorUUG TTG ""
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.colorUUU) != ''
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
317 -C $colours.colorUUU UUU ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
318 -C $colours.colorUUU TTT ""
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
319 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
320 #end if
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
321
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
322 </command>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
323 <inputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
324 <page>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
325 <param format="fasta" name="input" type="data" label="txt" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
326
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
327 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
328
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
329 <param name="outformat" type="select" label="Output format for image (or text report)" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
330 <option value="png" selected="True">PNG screen quality</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
331 <option value="png_print">High quality printable PNG</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
332 <option value="pdf">PDF</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
333 <option value="jpeg">JPG</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
334 <option value="eps">EPS</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
335 <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
336 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
337 <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
338 <option value="0" selected="True">0</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
339 <option value="1">+1</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
340 <option value="2">-1</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
341 <option value="3">reverse complement 0</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
342 <option value="4">reverse complement +1</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
343 <option value="5">reverse complement -1</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
344 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
345 <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
346 <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
347 <option value="True" selected="True">Yes</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
348 <option value="False">No</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
349 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
350 <param name="xlabel" label="X-axis label" type="text" size="50" value="" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
351 <param name="ylabel" label="Y-axis label" type="text" size="50" value="" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
352
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
353 <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.0" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
354
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
355
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
356 <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
357 <option value="True" selected="True">Yes</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
358 <option value="False">No</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
359 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
360 <param name="errorbars" type="select" display="radio" label="Display error bars?" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
361 <option value="True" selected="True">Yes</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
362 <option value="False">No</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
363 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
364 <conditional name="range">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
365 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
366 <option value="complete" selected="true">complete sequence</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
367 <option value="part">Only use a part of the sequence</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
368 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
369 <when value="complete">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
370 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
371 <when value="part">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
372 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
373 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
374 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
375 <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
376 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
377 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
378 </conditional>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
379 <conditional name="comp">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
380 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
381
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
382 <option value="equiprobable" >equiprobable</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
383 <option value="none" >none</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
384 <option value="file">from file</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
385
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
386 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
387 <when value="auto">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
388 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
389 <when value="equiprobable">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
390 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
391 <when value="none">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
392 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
393 <when value="file">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
394 <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
395 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
396
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
397 </conditional>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
398 <conditional name="colours">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
399 <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
400 <option value="no" selected="true">Default colours</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
401 <option value="part">Set your own.</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
402 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
403 <when value="no">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
404 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
405 <when value="part">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
406
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
407 <param name="colorAAA" size="10" type="text" value="" label="AAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
408 <param name="colorAAC" size="10" type="text" value="" label="AAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
409 <param name="colorAAG" size="10" type="text" value="" label="AAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
410 <param name="colorAAU" size="10" type="text" value="" label="AAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
411 <param name="colorACA" size="10" type="text" value="" label="ACA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
412 <param name="colorACC" size="10" type="text" value="" label="ACC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
413 <param name="colorACG" size="10" type="text" value="" label="ACG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
414 <param name="colorACU" size="10" type="text" value="" label="ACU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
415 <param name="colorAGA" size="10" type="text" value="" label="AGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
416 <param name="colorAGC" size="10" type="text" value="" label="AGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
417 <param name="colorAGG" size="10" type="text" value="" label="AGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
418 <param name="colorAGU" size="10" type="text" value="" label="AGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
419 <param name="colorAUA" size="10" type="text" value="" label="AUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
420 <param name="colorAUC" size="10" type="text" value="" label="AUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
421 <param name="colorAUG" size="10" type="text" value="" label="AUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
422 <param name="colorAUU" size="10" type="text" value="" label="AUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
423 <param name="colorCAA" size="10" type="text" value="" label="CAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
424 <param name="colorCAC" size="10" type="text" value="" label="CAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
425 <param name="colorCAG" size="10" type="text" value="" label="CAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
426 <param name="colorCAU" size="10" type="text" value="" label="CAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
427 <param name="colorCCA" size="10" type="text" value="" label="CCA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
428 <param name="colorCCC" size="10" type="text" value="" label="CCC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
429 <param name="colorCCG" size="10" type="text" value="" label="CCG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
430 <param name="colorCCU" size="10" type="text" value="" label="CCU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
431 <param name="colorCGA" size="10" type="text" value="" label="CGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
432 <param name="colorCGC" size="10" type="text" value="" label="CGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
433 <param name="colorCGG" size="10" type="text" value="" label="CGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
434 <param name="colorCGU" size="10" type="text" value="" label="CGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
435 <param name="colorCUA" size="10" type="text" value="" label="CUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
436 <param name="colorCUC" size="10" type="text" value="" label="CUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
437 <param name="colorCUG" size="10" type="text" value="" label="CUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
438 <param name="colorCUU" size="10" type="text" value="" label="CUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
439 <param name="colorGAA" size="10" type="text" value="" label="GAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
440 <param name="colorGAC" size="10" type="text" value="" label="GAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
441 <param name="colorGAG" size="10" type="text" value="" label="GAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
442 <param name="colorGAU" size="10" type="text" value="" label="GAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
443 <param name="colorGCA" size="10" type="text" value="" label="GCA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
444 <param name="colorGCC" size="10" type="text" value="" label="GCC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
445 <param name="colorGCG" size="10" type="text" value="" label="GCG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
446 <param name="colorGCU" size="10" type="text" value="" label="GCU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
447 <param name="colorGGA" size="10" type="text" value="" label="GGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
448 <param name="colorGGC" size="10" type="text" value="" label="GGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
449 <param name="colorGGG" size="10" type="text" value="" label="GGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
450 <param name="colorGGU" size="10" type="text" value="" label="GGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
451 <param name="colorGUA" size="10" type="text" value="" label="GUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
452 <param name="colorGUC" size="10" type="text" value="" label="GUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
453 <param name="colorGUG" size="10" type="text" value="" label="GUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
454 <param name="colorGUU" size="10" type="text" value="" label="GUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
455 <param name="colorUAA" size="10" type="text" value="" label="UAA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
456 <param name="colorUAC" size="10" type="text" value="" label="UAC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
457 <param name="colorUAG" size="10" type="text" value="" label="UAG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
458 <param name="colorUAU" size="10" type="text" value="" label="UAU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
459 <param name="colorUCA" size="10" type="text" value="" label="UCA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
460 <param name="colorUCC" size="10" type="text" value="" label="UCC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
461 <param name="colorUCG" size="10" type="text" value="" label="UCG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
462 <param name="colorUCU" size="10" type="text" value="" label="UCU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
463 <param name="colorUGA" size="10" type="text" value="" label="UGA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
464 <param name="colorUGC" size="10" type="text" value="" label="UGC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
465 <param name="colorUGG" size="10" type="text" value="" label="UGG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
466 <param name="colorUGU" size="10" type="text" value="" label="UGU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
467 <param name="colorUUA" size="10" type="text" value="" label="UUA" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
468 <param name="colorUUC" size="10" type="text" value="" label="UUC" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
469 <param name="colorUUG" size="10" type="text" value="" label="UUG" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
470 <param name="colorUUU" size="10" type="text" value="" label="UUU" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
471
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
472
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
473
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
474 </when>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
475
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
476 </conditional>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
477 <param name="size" type="select" label="Output CodonLogo size" >
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
478 <option value="large" selected="True">Large</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
479 <option value="medium">Medium</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
480 <option value="small">Small</option>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
481 </param>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
482
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
483 </page>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
484 </inputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
485 <outputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
486 <data format="pdf" name="output" label="${logoname}_output.${outformat}">
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
487 <change_format>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
488 <when input="outformat" value="png_print" format="png" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
489 <when input="outformat" value="png" format="png" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
490 <when input="outformat" value="jpeg" format="jpg" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
491 <when input="outformat" value="eps" format="eps" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
492 <when input="outformat" value="txt" format="txt" />
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
493 </change_format>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
494 </data>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
495 </outputs>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
496 <help>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
497
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
498 **Note**
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
499
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
500 This tool uses CodonLogo in Galaxy to generate a sequence logo from a provided alignment.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
501 The input file must be an alignment in your current history.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
502 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
503
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
504 A typical output looks like this
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
505
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
506 .. image:: ./static/images/CodonLogoExample.png
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
507
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
508 ----
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
509
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
510 **Warning about input files**
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
511
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
512 The program used by this tool will fail if your alignment files are not all the same length.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
513
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
514 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
515 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
516 sequences are the same length!
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
517
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
518 Files must first be converted to fasta format in order to be used with this tool.
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
519
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
520 ----
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
521
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
522 The default colour scheme is based on associated amino acid types:
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
523
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
524 Polar positive
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
525 H, K, R -Light Blue
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
526
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
527 Polar negative
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
528 D, E -Red
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
529
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
530 Polar neutral
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
531 S, T, N, Q -Green
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
532
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
533 Non-polar aliphatic
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
534 A, V, L, I, M -Blue
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
535
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
536 Non-polar aromatic
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
537 F, W, Y -Magenta
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
538 P, G -Brown
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
539 C -Yellow
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
540
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
541 Stop codons -Black
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
542
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
543
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
544 **Attribution**
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
545
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
546
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
547 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_
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
548
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
549 .. _Weblogo3: http://weblogo.berkeley.edu/
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
550 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
551 .. _CodonLogo: http://recode.ucc.ie/CodonLogo
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
552
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
553 </help>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
554
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
555 </tool>
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
556
4d47ab2b7bcc Uploaded
davidmurphy
parents:
diff changeset
557