Mercurial > repos > iuc > ggplot2_violin

annotate ggplot_violin.xml @ 9:8aafe85a86c7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
author iuc
date Mon, 30 Sep 2024 15:39:53 +0000
parents c212018cbadd
children a931d304f1b3
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1921f864cc7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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1 <tool id="ggplot2_violin" name="Violin plot w ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <macros>
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3 <import>macros.xml</import>
c5bd100a1d3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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4 </macros>
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8aafe85a86c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
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5 <expand macro="bio_tools"/>
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c5bd100a1d3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.4.4">r-reshape2</requirement>
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8 <requirement type="package" version="2.1.0">r-svglite</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 cat '$script' &&
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12 Rscript '$script'
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="script"><![CDATA[
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16 @R_INIT@
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17
c5bd100a1d3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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18 ## Import library
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19 library(reshape2)
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20 library(ggplot2)
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21
2
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22 ## Automatically scaled y axis or user defined
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23 ## marco not possible because on y asis relevent
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24 #if $adv.scaling.plot_scaling == "Automatic"
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25 gg_scaley = NULL
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26 #else
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27 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
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28 #end if
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30 integrated <- read.csv('$input1', sep='\t', header=TRUE)
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31 input <- melt(integrated)
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33 @TRANSFORM@
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34
2
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35 @THEME@
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37 @LEGEND@
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38
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39 #if $adv.drawquartiles == "none"
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40 gg_quartile = NULL
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41 #else
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42 gg_quartile = c(0.25, 0.5, 0.75)
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43 #end if
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44
2
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45 ## add advanced plotting options for final plot
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46 plot_out <- ggplot(input, aes(variable, value)) +
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47 geom_violin(scale = "area", colour = '$adv.ggcolor', fill = '$adv.ggfill', draw_quantiles = gg_quartile) +
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48 gg_scaley + gg_legend + gg_theme + xlab('$xlab') + ylab('$ylab') + ggtitle('$title')
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49
2
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50 @SAVE_OUTPUT@
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51 ]]></configfile>
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52 </configfiles>
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53 <inputs>
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54 <param name="input1" type="data" format="tabular" label="Input in tabular format"
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55 help="Column headers are requirement. These will be the columns that are plotted."/>
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56 <expand macro="title" />
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57 <expand macro="xy_lab" />
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58 <section name="adv" title="Advanced Options" expanded="false">
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59 <param name="drawquartiles" type="select" label="Indicate quartiles of your data">
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60 <option value="none">Plot the data without indicating quartiles</option>
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61 <option value="indicate">Draw lines to indicate each quartile</option>
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62 </param>
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63 <param name="ggfill" type="select" label="Violin color options">
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64 <option value="blue" selected="true">Default (Blue)</option>
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65 <option value="black">Black</option>
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66 <option value="red">Red</option>
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67 <option value="white">White</option>
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68 <option value="orange">Orange</option>
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69 <option value="yellow">Yellow</option>
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70 <option value="green">Green</option>
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71 <option value="purple">Purple</option>
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72 <option value="magenta">Magenta</option>
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73 <option value="cyan">Cyan</option>
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74 <option value="grey">Grey</option>
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75 <option value="gold">Gold</option>
0
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76 </param>
2
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77 <param name="ggcolor" type="select" label="Violin border options">
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78 <option value="yellow" selected="true">Default (Yellow)</option>
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79 <option value="black">Black</option>
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80 <option value="red">Red</option>
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81 <option value="white">White</option>
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82 <option value="blue">Blue</option>
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83 <option value="orange">Orange</option>
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84 <option value="green">Green</option>
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85 <option value="purple">Purple</option>
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86 <option value="magenta">Magenta</option>
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87 <option value="cyan">Cyan</option>
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88 <option value="grey">Grey</option>
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89 <option value="gold">Gold</option>
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90 </param>
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91 <expand macro="transform" />
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92 <expand macro="xy_scaling" />
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93 <expand macro="theme" />
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94 <expand macro="legend" />
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95 </section>
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96 <section name="out" title="Output Options" expanded="true">
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97 <expand macro="dimensions" />
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98 </section>
0
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99 </inputs>
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100 <outputs>
2
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101 <expand macro="additional_output" />
0
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102 </outputs>
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103 <tests>
9
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104 <test expect_num_outputs="2">
0
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105 <param name="input1" value="mtcars.txt" ftype="tabular"/>
2
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106 <param name="additional_output_format" value="pdf" />
9
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107 <output name="output2" file="ggplot_violin_result1.pdf" ftype="pdf" compare="sim_size"/>
0
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108 </test>
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109 </tests>
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110 <help><![CDATA[
2
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111 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.
0
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112 ]]></help>
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113 <expand macro="citations"/>
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114 </tool>