Mercurial > repos > iuc > ggplot2_histogram

annotate ggplot_histogram.xml @ 0:742d6f7a55b1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
author iuc
date Tue, 22 Aug 2017 06:39:55 -0400
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742d6f7a55b1 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_histogram" name="Histogram w ggplot2" version="@VERSION@">
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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2 <macros>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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3 <import>macros.xml</import>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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4 </macros>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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5 <expand macro="requirements">
742d6f7a55b1 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>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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7 </expand>
742d6f7a55b1 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[
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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9 cat '$script' &&
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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10 Rscript '$script'
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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11 ]]></command>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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12 <configfiles>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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13 <configfile name="script"><![CDATA[
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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15 @R_INIT@
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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17 ## Import library
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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18 library("reshape2")
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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19 library("ggplot2")
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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21 integrated <- read.csv('$input1', sep='\t', header=TRUE)
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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22 input <- melt(integrated)
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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24 ## Show/hide legend
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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25 #if $legend == "yes"
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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26 gg_legend = NULL
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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27 #else
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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28 gg_legend = theme(legend.position="none")
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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29 #end if
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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30
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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31 ## density
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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32 #if $density == "counts"
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33 gg_density = ggplot(input,aes(value, color=variable))
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 gg_freq = NULL
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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35 #elif $density == "nfreq"
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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36 gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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37 gg_freq = NULL
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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38 #elif $density == "freq"
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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39 gg_density = ggplot(input,aes(value, color=variable))
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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40 gg_freq = aes(y=..count../sum(..count..))
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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41 #end if
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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42
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43 @XY_SCALING@
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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44
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45 gg_width = $with_output_dim
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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46 gg_height = $height_output_dim
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47
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48
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49 @TRANSFORM@
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50
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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51 #if $facet == "facet"
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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52 gg_facet = facet_wrap(~ variable)
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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53 #else
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54 gg_facet = NULL
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55 #end if
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56
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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57 #if $coloring.colorscheme == "Default"
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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58 gg_colorscale = NULL
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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59 #else
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60 gg_colorscale = scale_color_brewer(palette=$coloring.colors, direction=$coloring.colororder)
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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61 #end if
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62
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63 gg_density+
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64 geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size)+gg_facet+gg_colorscale+
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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65 gg_scalex+gg_scaley+theme_bw()+xlab('$xlab')+ylab('$ylab')+gg_legend+ggtitle('$title')
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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66
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67 ggsave(file='Rplot.pdf')
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68 dev.off()
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69 ]]></configfile>
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70 </configfiles>
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71 <inputs>
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72 <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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73 <expand macro="title" />
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74 <expand macro="xy_lab" />
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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75 <param name="size" type="float" value="1.0" label="relative line width" />
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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76 <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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77
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78 <expand macro="transform" />
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79
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80 <param name="density" type="select" label="Advanced - plot counts or density">
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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81 <option value="counts">Plot counts on the y-axis</option>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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82 <option value="freq">Plot frequency on the y-axis</option>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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83 <option value="nfreq">Plot normalized frequency on the y-axis</option>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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84 </param>
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85 <param name="facet" type="select" label="Advanced - faceting">
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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86 <option value="none">Plot my groups on one plot</option>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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87 <option value="facet">Plot my groups on individual plots</option>
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88 </param>
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89 <conditional name="coloring">
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90 <param name="colorscheme" type="select" label="Advanced - coloring groups" >
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91 <option value="Default" selected="True">No thanks - just use the default scheme to color code my groups (columns)</option>
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92 <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
742d6f7a55b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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93 </param>
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94 <when value="Default">
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95 </when>
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96 <when value="Defined">
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97 <expand macro="colors" />
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98 <param name="colororder" type="select" label="Reverse color scheme" >
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99 <option value="1">Default order of color scheme</option>
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100 <option value="-1">Reverse the order of my color scheme</option>
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101 </param>
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102 </when>
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103 </conditional>
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104 <expand macro="xy_scaling" />
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105 <expand macro="dimensions" />
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106 <param name="legend" type="select" label="Legend options">
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107 <option value="yes">Include legend on plot</option>
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108 <option value="no">Hide legend</option>
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109 </param>
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110 </inputs>
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111 <outputs>
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112 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/>
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113 ToDo: It would be nice to have different output formats for all tools
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114 -->
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115 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
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116 </outputs>
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117 <tests>
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118 <test>
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119 <param name="input1" value="mtcars.txt"/>
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120 <output name="output1" file="ggplot_histogram_result1.pdf" compare="sim_size"/>
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124
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125 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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126
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127 Input data example:
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128 ID Cond_A Cond_B
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129 gene_A 10 15
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130 gene_B 8 12
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131 gene_C 10 15
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132 gene_D 6 9
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133 gene_E 9 13.5
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134 gene_F 8 12
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135
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136 ]]></help>
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137 <expand macro="citations"/>
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138 </tool>