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1 <tool id="2" name="Violin plot w ggplot2" version="0.1.2">
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2 <requirements>
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3 <requirement type="package">r-getopt</requirement>
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4 <requirement type="package">r-ggplot2</requirement>
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5 <requirement type="package">r-reshape2</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript ${__tool_directory__}/ggplotscriptviolin.R --input "$input1" --title "$title" --xlab "$xlab" --ylab "$ylab" --drawquartiles "$quartiles.drawquartiles" --ggfill "$fill.ggfill" --ggcolor "$color.ggcolor" --transform "$transformation.transform" --scaling "$scaling.Plot_scaling" --output "Rplot.pdf"
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12
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13
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14 #if str( $scaling.Plot_scaling ) == "Defined":
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15 --yaxismin=${scaling.yaxismin}
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16 --yaxismax=${scaling.yaxismax}
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17 #else:
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18 --yaxismin=2
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19 --yaxismax=3
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20 #end if
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21
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22
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23 ]]></command>
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24 <inputs>
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25 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
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26 <param name="title" size="30" type="text" format="txt" />
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27 <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x axis"/>
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28 <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y axis"/>
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29 <conditional name="scaling">
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30 <param name="Plot_scaling" type="select" label="Advanced - Axis scaling">
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31 <option value="Automatic" selected="True">Automatic axis scaling</option>
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32 <option value="Defined">User deined axis scales</option>
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33 </param>
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34 <when value="Automatic">
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35 </when>
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36 <when value="Defined">
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37 <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" />
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38 <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" />
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39 </when>
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40 </conditional>
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41 <conditional name="transformation">
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42 <param name="transform" type="select" label="Advanced - log transformation">
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43 <option value="none">Plot the data as it is</option>
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44 <option value="log2">Log2(value) transform my data</option>
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45 <option value="log2plus1">Log2(value+1) transform my data</option>
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46 <option value="log10">Log10(value) transform my data</option>
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47 <option value="log10plus1">Log10(value+1) transform my data</option>
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48 </param>
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49 </conditional>
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50 <conditional name="quartiles">
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51 <param name="drawquartiles" type="select" label="Advanced - indicate quartiles of your data">
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52 <option value="none">Plot the data without indicating quartiles</option>
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53 <option value="indicate">Draw lines to indicate each quartile</option>
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54 </param>
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55 </conditional>
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56 <conditional name="fill">
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57 <param name="ggfill" type="select" label="Advanced - violin color options">
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58 <option value="blue" selected="True">Default (Blue)</option>
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59 <option value="black">Black</option>
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60 <option value="red">Red</option>
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61 <option value="white">White</option>
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62 <option value="orange">Orange</option>
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63 <option value="yellow">Yellow</option>
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64 <option value="green">Green</option>
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65 <option value="purple">Purple</option>
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66 <option value="magenta">Magenta</option>
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67 <option value="cyan">Cyan</option>
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68 <option value="grey">Grey</option>
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69 <option value="gold">Gold</option>
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70 </param>
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71 </conditional>
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72 <conditional name="color">
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73 <param name="ggcolor" type="select" label="Advanced - violin border options">
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74 <option value="yellow" selected="True">Default (Yellow)</option>
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75 <option value="black">Black</option>
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76 <option value="red">Red</option>
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77 <option value="white">White</option>
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78 <option value="blue">Blue</option>
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79 <option value="orange">Orange</option>
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80 <option value="green">Green</option>
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81 <option value="purple">Purple</option>
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82 <option value="magenta">Magenta</option>
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83 <option value="cyan">Cyan</option>
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84 <option value="grey">Grey</option>
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85 <option value="gold">Gold</option>
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86 </param>
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87 </conditional>
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88 </inputs>
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89 <outputs>
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90 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> -->
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91 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="input1" value="input.txt"/>
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96 <output name="output1" file="Rplot.pdf"/>
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 Supply this tool with a text file with headers indicating the various groups to be plotted. This tool will sniff out each column with values that can be plotted and display the distribution of that data group. Note that columns may be excluded from this plot if they contain questionable characters.
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101
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102 ]]></help>
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103 <citations>
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104 <citation type="bibtex">
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105 @misc{renameTODO,
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106 author = {LastTODO, FirstTODO},
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107 year = {TODO},
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108 title = {TODO},
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109 url = {under construction},
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110 }</citation>
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111 </citations>
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112 </tool>
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