Mercurial > repos > iuc > ggplot2_violin

annotate ggplot_violin.xml @ 7:1921f864cc7b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
author iuc
date Tue, 23 Nov 2021 07:55:48 +0000
parents 7d78bc3a86f3
children c212018cbadd
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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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7d78bc3a86f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <expand macro="bio_tools"/>
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3 <macros>
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4 <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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5 </macros>
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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1921f864cc7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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7 <requirement type="package" version="1.4.4">r-reshape2</requirement>
1921f864cc7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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8 <requirement type="package" version="2.0.0">r-svglite</requirement>
0
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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)
1921f864cc7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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20 library(ggplot2)
0
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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 $adv.scaling.plot_scaling == "Automatic"
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25 gg_scaley = NULL
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26 #else
2
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27 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
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28 #end if
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29
c5bd100a1d3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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30 integrated <- read.csv('$input1', sep='\t', header=TRUE)
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31 input <- melt(integrated)
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32
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33 @TRANSFORM@
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34
2
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35 @THEME@
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36
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37 @LEGEND@
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38
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39 #if $adv.drawquartiles == "none"
0
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40 gg_quartile = NULL
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41 #else
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42 gg_quartile = c(0.25, 0.5, 0.75)
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43 #end if
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44
2
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45 ## add advanced plotting options for final plot
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46 plot_out <- ggplot(input, aes(variable, value)) +
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47 geom_violin(scale = "area", colour = '$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')
0
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49
2
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50 @SAVE_OUTPUT@
0
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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" />
2
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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 <conditional name="scaling">
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93 <param name="plot_scaling" type="select" label="Axis scaling">
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94 <option value="Automatic" selected="true">Automatic axis scaling</option>
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95 <option value="Defined">User deined axis scales</option>
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96 </param>
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97 <when value="Automatic" />
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98 <when value="Defined">
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99 <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
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100 <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
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101 </when>
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102 </conditional>
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103 <expand macro="xy_scaling" />
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104 <expand macro="theme" />
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105 <expand macro="legend" />
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106 </section>
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107 <section name="out" title="Output Options" expanded="true">
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108 <expand macro="dimensions" />
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109 </section>
0
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110 </inputs>
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111 <outputs>
2
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112 <expand macro="additional_output" />
0
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113 </outputs>
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114 <tests>
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115 <test>
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116 <param name="input1" value="mtcars.txt" ftype="tabular"/>
2
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117 <param name="additional_output_format" value="pdf" />
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118 <output name="output2" file="ggplot_violin_result1.pdf" compare="sim_size"/>
0
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119 </test>
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120 </tests>
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121 <help><![CDATA[
2
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122 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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123 ]]></help>
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124 <expand macro="citations"/>
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125 </tool>