Mercurial > repos > iuc > ggplot2_histogram

annotate ggplot_histogram.xml @ 4:1f0242e49a58 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
author iuc
date Sun, 24 Mar 2019 13:21:52 -0400
parents f52035800250
children 536078949ae4
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f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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1 <tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@+galaxy0">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements">
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6 <requirement type="package" version="1.4.3">r-reshape2</requirement>
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7 <requirement type="package" version="1.2.1">r-svglite</requirement>
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 cat '$script' &&
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11 Rscript '$script'
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="script"><![CDATA[
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15 @R_INIT@
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16
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17 ## Import library
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18 library(reshape2)
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19 library(ggplot2)
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21 integrated <- read.csv('$input1', sep='\t', header=TRUE)
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22 input <- melt(integrated)
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23
2
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24 @LEGEND@
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25
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26 ## density
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27 #if $adv.density == "counts"
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28 gg_density = ggplot(input,aes(value, color=variable))
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29 gg_freq = NULL
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30 #elif $adv.density == "nfreq"
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31 gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
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32 gg_freq = NULL
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33 #elif $adv.density == "freq"
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34 gg_density = ggplot(input,aes(value, color=variable))
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35 gg_freq = aes(y=..count../sum(..count..))
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36 #end if
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37
2
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38 @TRANSFORM@
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39
0
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40 @XY_SCALING@
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41
2
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42 @THEME@
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43
2
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44 #if $adv.facet == "facet"
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45 gg_facet = facet_wrap(~ variable)
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46 #else
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47 gg_facet = NULL
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48 #end if
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49
2
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50 #if $adv.coloring.colorscheme == "Default"
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51 gg_colorscale = NULL
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52 #else
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53 gg_colorscale = scale_color_brewer(palette=$adv.coloring.colors, direction=$adv.coloring.colororder)
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54 #end if
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55
2
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56 plot_out <- gg_density +
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57 geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size) + gg_facet + gg_colorscale +
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58 gg_scalex +
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59 gg_scaley +
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60 gg_theme +
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61 xlab('$xlab') +
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62 ylab('$ylab') +
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63 gg_legend +
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64 ggtitle('$title') +
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65 theme(plot.title = element_text(hjust = 0.5))
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66
2
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67 @SAVE_OUTPUT@
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68 ]]></configfile>
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69 </configfiles>
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70 <inputs>
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71 <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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72 <expand macro="title" />
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73 <expand macro="xy_lab" />
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74 <param name="size" type="float" value="1.0" label="relative line width" />
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75 <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/>
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76 <section name="adv" title="Advanced Options" expanded="false">
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77 <param name="density" type="select" label="Plot counts or density">
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78 <option value="counts">Plot counts on the y-axis</option>
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79 <option value="freq">Plot frequency on the y-axis</option>
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80 <option value="nfreq">Plot normalized frequency on the y-axis</option>
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81 </param>
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82 <param name="facet" type="select" label="Faceting">
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83 <option value="none">Plot my groups on one plot</option>
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84 <option value="facet">Plot my groups on individual plots</option>
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85 </param>
2
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86 <conditional name="coloring">
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87 <param name="colorscheme" type="select" label="Coloring groups" >
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88 <option value="Default" selected="true">No thanks - just use the default scheme to color code my groups (columns)</option>
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89 <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
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90 </param>
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91 <when value="Default">
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92 </when>
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93 <when value="Defined">
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94 <expand macro="colors" />
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95 <param name="colororder" type="select" label="Reverse color scheme" >
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96 <option value="1">Default order of color scheme</option>
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97 <option value="-1">Reverse the order of my color scheme</option>
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98 </param>
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99 </when>
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100 </conditional>
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101 <expand macro="transform" />
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102 <expand macro="xy_scaling" />
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103 <expand macro="theme" />
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104 <expand macro="legend" />
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105 </section>
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106 <section name="out" title="Output Options" expanded="true">
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107 <expand macro="dimensions" />
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108 </section>
0
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109 </inputs>
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110 <outputs>
2
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111 <expand macro="additional_output" />
0
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112 </outputs>
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113 <tests>
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114 <test>
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115 <param name="input1" value="mtcars.txt"/>
2
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116 <param name="additional_output_format" value="pdf" />
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117 <output name="output2" file="ggplot_histogram_result1.pdf" compare="sim_size"/>
0
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118 </test>
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119 </tests>
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120 <help><![CDATA[
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121 This tool will generate a histogram representing the distrinutions of each numerical column. Each column should have a descriptive header with no spaces, which will be used in the plot legend to represent the corresponding column (group).
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122
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123 Input data example:
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124 ID Cond_A Cond_B
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125 gene_A 10 15
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126 gene_B 8 12
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127 gene_C 10 15
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128 gene_D 6 9
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129 gene_E 9 13.5
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130 gene_F 8 12
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131 ]]></help>
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132 <expand macro="citations"/>
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133 </tool>