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comparison ggplot_histogram.xml @ 2:f52035800250 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
author iuc
date Mon, 11 Jun 2018 16:05:18 -0400
parents 9d060114554c
children 536078949ae4
comparison
equal deleted inserted replaced
1:d3d92fb20389 2:f52035800250
1 <tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@"> 1 <tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@+galaxy0">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements"> 5 <expand macro="requirements">
6 <requirement type="package" version="1.4.2">r-reshape2</requirement> 6 <requirement type="package" version="1.4.3">r-reshape2</requirement>
7 <requirement type="package" version="1.2.1">r-svglite</requirement>
7 </expand> 8 </expand>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 cat '$script' && 10 cat '$script' &&
10 Rscript '$script' 11 Rscript '$script'
11 ]]></command> 12 ]]></command>
12 <configfiles> 13 <configfiles>
13 <configfile name="script"><![CDATA[ 14 <configfile name="script"><![CDATA[
14
15 @R_INIT@ 15 @R_INIT@
16 16
17 ## Import library 17 ## Import library
18 library("reshape2") 18 library(reshape2)
19 library("ggplot2") 19 library(ggplot2)
20 20
21 integrated <- read.csv('$input1', sep='\t', header=TRUE) 21 integrated <- read.csv('$input1', sep='\t', header=TRUE)
22 input <- melt(integrated) 22 input <- melt(integrated)
23 23
24 ## Show/hide legend 24 @LEGEND@
25 #if $legend == "yes"
26 gg_legend = NULL
27 #else
28 gg_legend = theme(legend.position="none")
29 #end if
30 25
31 ## density 26 ## density
32 #if $density == "counts" 27 #if $adv.density == "counts"
33 gg_density = ggplot(input,aes(value, color=variable)) 28 gg_density = ggplot(input,aes(value, color=variable))
34 gg_freq = NULL 29 gg_freq = NULL
35 #elif $density == "nfreq" 30 #elif $adv.density == "nfreq"
36 gg_density = ggplot(input,aes(value, ..ncount.., color=variable)) 31 gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
37 gg_freq = NULL 32 gg_freq = NULL
38 #elif $density == "freq" 33 #elif $adv.density == "freq"
39 gg_density = ggplot(input,aes(value, color=variable)) 34 gg_density = ggplot(input,aes(value, color=variable))
40 gg_freq = aes(y=..count../sum(..count..)) 35 gg_freq = aes(y=..count../sum(..count..))
41 #end if 36 #end if
42 37
38 @TRANSFORM@
39
43 @XY_SCALING@ 40 @XY_SCALING@
44 41
45 gg_width = $with_output_dim 42 @THEME@
46 gg_height = $height_output_dim
47 43
48 44 #if $adv.facet == "facet"
49 @TRANSFORM@
50
51 #if $facet == "facet"
52 gg_facet = facet_wrap(~ variable) 45 gg_facet = facet_wrap(~ variable)
53 #else 46 #else
54 gg_facet = NULL 47 gg_facet = NULL
55 #end if 48 #end if
56 49
57 #if $coloring.colorscheme == "Default" 50 #if $adv.coloring.colorscheme == "Default"
58 gg_colorscale = NULL 51 gg_colorscale = NULL
59 #else 52 #else
60 gg_colorscale = scale_color_brewer(palette=$coloring.colors, direction=$coloring.colororder) 53 gg_colorscale = scale_color_brewer(palette=$adv.coloring.colors, direction=$adv.coloring.colororder)
61 #end if 54 #end if
62 55
63 gg_density+ 56 plot_out <- gg_density +
64 geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size)+gg_facet+gg_colorscale+ 57 geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size) + gg_facet + gg_colorscale +
65 gg_scalex+gg_scaley+theme_bw()+xlab('$xlab')+ylab('$ylab')+gg_legend+ggtitle('$title') 58 gg_scalex +
59 gg_scaley +
60 gg_theme +
61 xlab('$xlab') +
62 ylab('$ylab') +
63 gg_legend +
64 ggtitle('$title') +
65 theme(plot.title = element_text(hjust = 0.5))
66 66
67 ggsave(file='Rplot.pdf') 67 @SAVE_OUTPUT@
68 dev.off()
69 ]]></configfile> 68 ]]></configfile>
70 </configfiles> 69 </configfiles>
71 <inputs> 70 <inputs>
72 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/> 71 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
73 <expand macro="title" /> 72 <expand macro="title" />
74 <expand macro="xy_lab" /> 73 <expand macro="xy_lab" />
75 <param name="size" type="float" value="1.0" label="relative line width" /> 74 <param name="size" type="float" value="1.0" label="relative line width" />
76 <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/> 75 <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/>
77 76 <section name="adv" title="Advanced Options" expanded="false">
78 <expand macro="transform" /> 77 <param name="density" type="select" label="Plot counts or density">
79 78 <option value="counts">Plot counts on the y-axis</option>
80 <param name="density" type="select" label="Advanced - plot counts or density"> 79 <option value="freq">Plot frequency on the y-axis</option>
81 <option value="counts">Plot counts on the y-axis</option> 80 <option value="nfreq">Plot normalized frequency on the y-axis</option>
82 <option value="freq">Plot frequency on the y-axis</option>
83 <option value="nfreq">Plot normalized frequency on the y-axis</option>
84 </param>
85 <param name="facet" type="select" label="Advanced - faceting">
86 <option value="none">Plot my groups on one plot</option>
87 <option value="facet">Plot my groups on individual plots</option>
88 </param>
89 <conditional name="coloring">
90 <param name="colorscheme" type="select" label="Advanced - coloring groups" >
91 <option value="Default" selected="True">No thanks - just use the default scheme to color code my groups (columns)</option>
92 <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
93 </param> 81 </param>
94 <when value="Default"> 82 <param name="facet" type="select" label="Faceting">
95 </when> 83 <option value="none">Plot my groups on one plot</option>
96 <when value="Defined"> 84 <option value="facet">Plot my groups on individual plots</option>
97 <expand macro="colors" /> 85 </param>
98 <param name="colororder" type="select" label="Reverse color scheme" > 86 <conditional name="coloring">
99 <option value="1">Default order of color scheme</option> 87 <param name="colorscheme" type="select" label="Coloring groups" >
100 <option value="-1">Reverse the order of my color scheme</option> 88 <option value="Default" selected="true">No thanks - just use the default scheme to color code my groups (columns)</option>
101 </param> 89 <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
102 </when> 90 </param>
103 </conditional> 91 <when value="Default">
104 <expand macro="xy_scaling" /> 92 </when>
105 <expand macro="dimensions" /> 93 <when value="Defined">
106 <param name="legend" type="select" label="Legend options"> 94 <expand macro="colors" />
107 <option value="yes">Include legend on plot</option> 95 <param name="colororder" type="select" label="Reverse color scheme" >
108 <option value="no">Hide legend</option> 96 <option value="1">Default order of color scheme</option>
109 </param> 97 <option value="-1">Reverse the order of my color scheme</option>
98 </param>
99 </when>
100 </conditional>
101 <expand macro="transform" />
102 <expand macro="xy_scaling" />
103 <expand macro="theme" />
104 <expand macro="legend" />
105 </section>
106 <section name="out" title="Output Options" expanded="true">
107 <expand macro="dimensions" />
108 </section>
110 </inputs> 109 </inputs>
111 <outputs> 110 <outputs>
112 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> 111 <expand macro="additional_output" />
113 ToDo: It would be nice to have different output formats for all tools
114 -->
115 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
116 </outputs> 112 </outputs>
117 <tests> 113 <tests>
118 <test> 114 <test>
119 <param name="input1" value="mtcars.txt"/> 115 <param name="input1" value="mtcars.txt"/>
120 <output name="output1" file="ggplot_histogram_result1.pdf" compare="sim_size"/> 116 <param name="additional_output_format" value="pdf" />
117 <output name="output2" file="ggplot_histogram_result1.pdf" compare="sim_size"/>
121 </test> 118 </test>
122 </tests> 119 </tests>
123 <help><![CDATA[ 120 <help><![CDATA[
124
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). 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).
126 122
127 Input data example: 123 Input data example:
128 ID Cond_A Cond_B 124 ID Cond_A Cond_B
129 gene_A 10 15 125 gene_A 10 15
130 gene_B 8 12 126 gene_B 8 12
131 gene_C 10 15 127 gene_C 10 15
132 gene_D 6 9 128 gene_D 6 9
133 gene_E 9 13.5 129 gene_E 9 13.5
134 gene_F 8 12 130 gene_F 8 12
135
136 ]]></help> 131 ]]></help>
137 <expand macro="citations"/> 132 <expand macro="citations"/>
138 </tool> 133 </tool>