Mercurial > repos > iuc > ggplot2_histogram

comparison 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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children 7d85541cba47
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-1:000000000000 0:742d6f7a55b1
1 <tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="requirements">
6 <requirement type="package" version="1.4.2">r-reshape2</requirement>
7 </expand>
8 <command detect_errors="exit_code"><![CDATA[
9 cat '$script' &&
10 Rscript '$script'
11 ]]></command>
12 <configfiles>
13 <configfile name="script"><![CDATA[
14
15 @R_INIT@
16
17 ## Import library
18 library("reshape2")
19 library("ggplot2")
20
21 integrated <- read.csv('$input1', sep='\t', header=TRUE)
22 input <- melt(integrated)
23
24 ## Show/hide legend
25 #if $legend == "yes"
26 gg_legend = NULL
27 #else
28 gg_legend = theme(legend.position="none")
29 #end if
30
31 ## density
32 #if $density == "counts"
33 gg_density = ggplot(input,aes(value, color=variable))
34 gg_freq = NULL
35 #elif $density == "nfreq"
36 gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
37 gg_freq = NULL
38 #elif $density == "freq"
39 gg_density = ggplot(input,aes(value, color=variable))
40 gg_freq = aes(y=..count../sum(..count..))
41 #end if
42
43 @XY_SCALING@
44
45 gg_width = $with_output_dim
46 gg_height = $height_output_dim
47
48
49 @TRANSFORM@
50
51 #if $facet == "facet"
52 gg_facet = facet_wrap(~ variable)
53 #else
54 gg_facet = NULL
55 #end if
56
57 #if $coloring.colorscheme == "Default"
58 gg_colorscale = NULL
59 #else
60 gg_colorscale = scale_color_brewer(palette=$coloring.colors, direction=$coloring.colororder)
61 #end if
62
63 gg_density+
64 geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size)+gg_facet+gg_colorscale+
65 gg_scalex+gg_scaley+theme_bw()+xlab('$xlab')+ylab('$ylab')+gg_legend+ggtitle('$title')
66
67 ggsave(file='Rplot.pdf')
68 dev.off()
69 ]]></configfile>
70 </configfiles>
71 <inputs>
72 <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" />
74 <expand macro="xy_lab" />
75 <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"/>
77
78 <expand macro="transform" />
79
80 <param name="density" type="select" label="Advanced - plot counts or density">
81 <option value="counts">Plot counts 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>
94 <when value="Default">
95 </when>
96 <when value="Defined">
97 <expand macro="colors" />
98 <param name="colororder" type="select" label="Reverse color scheme" >
99 <option value="1">Default order of color scheme</option>
100 <option value="-1">Reverse the order of my color scheme</option>
101 </param>
102 </when>
103 </conditional>
104 <expand macro="xy_scaling" />
105 <expand macro="dimensions" />
106 <param name="legend" type="select" label="Legend options">
107 <option value="yes">Include legend on plot</option>
108 <option value="no">Hide legend</option>
109 </param>
110 </inputs>
111 <outputs>
112 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/>
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>
117 <tests>
118 <test>
119 <param name="input1" value="mtcars.txt"/>
120 <output name="output1" file="ggplot_histogram_result1.pdf" compare="sim_size"/>
121 </test>
122 </tests>
123 <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).
126
127 Input data example:
128 ID Cond_A Cond_B
129 gene_A 10 15
130 gene_B 8 12
131 gene_C 10 15
132 gene_D 6 9
133 gene_E 9 13.5
134 gene_F 8 12
135
136 ]]></help>
137 <expand macro="citations"/>
138 </tool>