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1 <tool id="rgweblogo3" name="Sequence Logo" version="0.5">
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2 <stdio>
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3 <regex match=".*" source="both" level="warning" description="chatter from weblogo:"/>
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4 </stdio>
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5 <requirements>
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6 <requirement type="package" version="3.3">package_weblogo</requirement>
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7 <requirement type="package" version="1.7.1">numpy</requirement>
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8 <requirement type="package" version="9.07">ghostscript</requirement>
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9 </requirements>
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10 <description>Generator from fasta</description>
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11 <command interpreter="python">
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12 rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"
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13 #if $range.mode == 'part'
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14 -l "$range.seqstart" -u "$range.seqend"
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15 #end if
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16 </command>
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17 <inputs>
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18 <page>
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19 <param format="fasta" name="input" type="data" label="Fasta File" />
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20 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" />
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21 <param name="outformat" type="select" label="Output format for image (or text report)" >
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22 <option value="png" selected="True">PNG screen quality</option>
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23 <option value="png_print">High quality printable PNG</option>
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24 <option value="pdf">PDF</option>
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25 <option value="jpeg">JPG</option>
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26 <option value="eps">EPS</option>
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27 <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
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28 </param>
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29 <param name="units" type="select" label="Display Units"
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30 help="What the height of each logo element depicts - eg bits of entropy (default)">
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31 <option value="bits" selected="True">Entropy (bits)</option>
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32 <option value="probability">Probability</option>
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33 <option value="nats">Nats</option>
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34 <option value="kT">kT</option>
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35 <option value="kJ/mol">kJ/mol</option>
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36 <option value="kcal/mol">kcal/mol</option>
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37 </param>
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38 <param name="colours" type="select" label="Colour scheme for output Sequence Logo"
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39 help="Note that some of these only make sense for protein sequences!">
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40 <option value="auto" selected="True">Default automatic colour selection</option>
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41 <option value="base pairing">Base pairing</option>
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42 <option value="charge">Charge colours</option>
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43 <option value="chemistry">Chemistry colours</option>
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44 <option value="classic">Classical colours</option>
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45 <option value="hydrophobicity">Hydrophobicity</option>
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46 <option value="monochrome">monochrome</option>
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47 </param>
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48
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49
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50 <conditional name="range">
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51 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
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52 <option value="complete" selected="true">complete sequence</option>
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53 <option value="part">Only use a part of the sequence</option>
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54 </param>
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55 <when value="complete">
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56 </when>
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57 <when value="part">
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58 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
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59 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
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60 </param>
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61 <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" >
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62 </param>
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63 </when>
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64 </conditional>
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65 <param name="size" type="select" label="Output weblogo size" >
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66 <option value="large" selected="True">Large</option>
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67 <option value="medium">Medium</option>
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68 <option value="small">Small</option>
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69 </param>
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70 </page>
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71 </inputs>
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72 <outputs>
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73 <data format="pdf" name="output" label="${logoname}.${outformat}">
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74 <change_format>
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75 <when input="outformat" value="png_print" format="png" />
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76 <when input="outformat" value="png" format="png" />
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77 <when input="outformat" value="jpeg" format="jpg" />
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78 <when input="outformat" value="eps" format="eps" />
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79 <when input="outformat" value="txt" format="txt" />
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80 </change_format>
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="input" value="rgClustal_testout.fasta" />
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86 <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
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87 <param name = "outformat" value="jpeg" />
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88 <param name = "mode" value="complete" />
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89 <param name = "size" value="medium" />
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90 <param name = "colours" value="auto" />
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91 <param name = "units" value="bits" />
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92 <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
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93 </test>
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94 <test>
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95 <param name="input" value="rgClustal_testout.fasta" />
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96 <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
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97 <param name = "outformat" value="png" />
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98 <param name = "mode" value="complete" />
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99 <param name = "size" value="medium" />
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100 <param name = "colours" value="auto" />
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101 <param name = "units" value="probability" />
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102 <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
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103 </test>
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104 </tests>
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105 <help>
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106
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107 **Note**
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108
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109 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
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110
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111 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
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112 it in to this tool.
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113
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114 A typical output looks like this
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115
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116 .. image:: $PATH_TO_IMAGES/rgWebLogo3_test.jpg
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117
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118 ----
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119
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120 **Warning about input Fasta format files**
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121
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122 The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
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123 and refuse to call the weblogo3 executable if irregular length sequences are detected.
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124
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125 Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file
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126 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
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127 sequences are exactly the same length!
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128
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129
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130 **Attribution**
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131
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132 Weblogo attribution and associated documentation are available at Weblogo3_
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133
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134 This Galaxy wrapper calls their software so depends on it and their license for your legal comfort.
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135 The wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
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136
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137 .. _Weblogo3: http://weblogo.threeplusone.com/manual.html
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138
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139 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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140
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141 </help>
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142
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143 </tool>
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144
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145
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