Mercurial > repos > iuc > ggplot2_violin

annotate ggplot_violin.xml @ 1:d85535076554 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 97544038b04c02170ab82877db666fa3022e4469
author iuc
date Tue, 29 Aug 2017 09:02:49 -0400
parents a597d59df9ee
children 43778344b955
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a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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1 <tool id="ggplot2_violin" name="Violin plot w ggplot2" version="@VERSION@">
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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2 <macros>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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3 <import>macros.xml</import>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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4 </macros>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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5 <expand macro="requirements">
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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6 <requirement type="package" version="1.4.2">r-reshape2</requirement>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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7 </expand>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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8 <command detect_errors="exit_code"><![CDATA[
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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9 cat '$script' &&
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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10 Rscript '$script' &&
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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11 mv output_plot.pdf $output1
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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12 ]]></command>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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13 <configfiles>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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14 <configfile name="script"><![CDATA[
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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15
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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16 @R_INIT@
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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17
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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18 ## Import library
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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19 library("reshape2")
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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20 library("ggplot2")
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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21
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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22 ## Choose between automatically scaled x and y axis or user defined
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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23 #if $scaling.plot_scaling == "Automatic"
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24 gg_scaley = NULL
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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25 #else
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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26 gg_scaley = ylim($scaling.yaxismin, $scaling.yaxismax)
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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27 #end if
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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28
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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29 integrated <- read.csv('$input1', sep='\t', header=TRUE)
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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30 input <- melt(integrated)
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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31
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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32 @TRANSFORM@
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 #if $drawquartiles == "none"
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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35 gg_quartile = NULL
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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36 #else
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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37 gg_quartile = c(0.25, 0.5, 0.75)
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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38 #end if
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39
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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40
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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41 ggplot(input, aes(variable, value)) + geom_violin(scale = "area", colour = '$ggcolor', fill = '$ggfill', draw_quantiles = gg_quartile) +
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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42 gg_scaley + theme_bw() + xlab('$xlab') + ylab('$ylab') + ggtitle('$title')
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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43
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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44 ggsave(file='output_plot.pdf')
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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45 dev.off()
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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46
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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47 ]]></configfile>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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48 </configfiles>
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49 <inputs>
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50 <param name="input1" type="data" format="tabular" label="Input in tabular format"
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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51 help="Column headers are requirement. These will be the columns that are plotted."/>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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52 <expand macro="title" />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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53 <expand macro="xy_lab" />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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54 <conditional name="scaling">
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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55 <param name="plot_scaling" type="select" label="Advanced - Axis scaling">
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56 <option value="Automatic" selected="True">Automatic axis scaling</option>
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57 <option value="Defined">User deined axis scales</option>
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58 </param>
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59 <when value="Automatic" />
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60 <when value="Defined">
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61 <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
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62 <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
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63 </when>
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64 </conditional>
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65 <expand macro="transform" />
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66 <param name="drawquartiles" type="select" label="Advanced - indicate quartiles of your data">
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67 <option value="none">Plot the data without indicating quartiles</option>
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68 <option value="indicate">Draw lines to indicate each quartile</option>
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69 </param>
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70 <param name="ggfill" type="select" label="Advanced - violin color options">
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71 <option value="blue" selected="True">Default (Blue)</option>
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72 <option value="black">Black</option>
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73 <option value="red">Red</option>
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74 <option value="white">White</option>
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75 <option value="orange">Orange</option>
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76 <option value="yellow">Yellow</option>
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77 <option value="green">Green</option>
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78 <option value="purple">Purple</option>
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79 <option value="magenta">Magenta</option>
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80 <option value="cyan">Cyan</option>
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81 <option value="grey">Grey</option>
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82 <option value="gold">Gold</option>
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83 </param>
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84 <param name="ggcolor" type="select" label="Advanced - violin border options">
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85 <option value="yellow" selected="True">Default (Yellow)</option>
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86 <option value="black">Black</option>
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87 <option value="red">Red</option>
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88 <option value="white">White</option>
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89 <option value="blue">Blue</option>
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90 <option value="orange">Orange</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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91 <option value="green">Green</option>
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92 <option value="purple">Purple</option>
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93 <option value="magenta">Magenta</option>
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94 <option value="cyan">Cyan</option>
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95 <option value="grey">Grey</option>
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96 <option value="gold">Gold</option>
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97 </param>
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98 </inputs>
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99 <outputs>
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100 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="input1" value="mtcars.txt" ftype="tabular"/>
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105 <output name="output1" file="ggplot_violin_result1.pdf" compare="sim_size"/>
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 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.
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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110
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111 ]]></help>
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112 <expand macro="citations"/>
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113 </tool>