|
4
|
1 <tool name="plotter" id="plotter" version="0.01">
|
|
|
2 <!--Source in git at: https://github.com/fubar2/toolfactory-->
|
|
|
3 <!--Created by planemo@galaxyproject.org at 31/03/2021 10:58:49 using the Galaxy Tool Factory.-->
|
|
|
4 <description>Makes random plots</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement version="" type="package">r-base</requirement>
|
|
|
7 </requirements>
|
|
|
8 <stdio>
|
|
|
9 <exit_code range="1:" level="fatal"/>
|
|
|
10 </stdio>
|
|
|
11 <expand macro="stdio"/>
|
|
|
12 <version_command><![CDATA[echo "0.01"]]></version_command>
|
|
|
13 <command><![CDATA[Rscript
|
|
|
14 $runme
|
|
|
15 "$nplot"]]></command>
|
|
|
16 <configfiles>
|
|
|
17 <configfile name="runme"><![CDATA[
|
|
|
18 \# demo
|
|
|
19 args = commandArgs(trailingOnly=TRUE)
|
|
|
20 if (length(args)==0) {
|
|
|
21 n_plots = 3
|
|
|
22 } else {
|
|
|
23 n_plots = as.integer(args[1]) }
|
|
|
24 dir.create('plots')
|
|
|
25 for (i in 1:n_plots) {
|
|
|
26 foo = runif(100)
|
|
|
27 bar = rnorm(100)
|
|
|
28 bar = foo + 0.05*bar
|
|
|
29 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
|
|
|
30 plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
|
|
|
31 dev.off()
|
|
|
32 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
|
|
|
33 bar = as.matrix(foo)
|
|
|
34 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
|
|
|
35 heatmap(bar,main='Random Heatmap')
|
|
|
36 dev.off()
|
|
|
37 }
|
|
|
38
|
|
|
39 ]]></configfile>
|
|
|
40 </configfiles>
|
|
|
41 <inputs>
|
|
|
42 <param name="nplot" type="text" value="3" label="Number of random plots pairs to draw" help=""/>
|
|
|
43 </inputs>
|
|
|
44 <outputs>
|
|
|
45 <collection name="plots" type="list" label="Plots">
|
|
|
46 <discover_datasets pattern="__name_and_ext__" directory="plots" visible="false"/>
|
|
|
47 </collection>
|
|
|
48 </outputs>
|
|
|
49 <tests>
|
|
|
50 <test>
|
|
|
51 <param name="nplot" value="3"/>
|
|
|
52 <output_collection name="plots"/>
|
|
|
53 </test>
|
|
|
54 </tests>
|
|
|
55 <help><![CDATA[
|
|
|
56
|
|
|
57 **What it Does**
|
|
|
58
|
|
|
59 Makes plots into a collection demonstration
|
|
|
60
|
|
|
61
|
|
|
62
|
|
|
63 ------
|
|
|
64
|
|
|
65
|
|
|
66 Script::
|
|
|
67
|
|
|
68 # demo
|
|
|
69 args = commandArgs(trailingOnly=TRUE)
|
|
|
70 if (length(args)==0) {
|
|
|
71 n_plots = 3
|
|
|
72 } else {
|
|
|
73 n_plots = as.integer(args[1]) }
|
|
|
74 dir.create('plots')
|
|
|
75 for (i in 1:n_plots) {
|
|
|
76 foo = runif(100)
|
|
|
77 bar = rnorm(100)
|
|
|
78 bar = foo + 0.05*bar
|
|
|
79 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
|
|
|
80 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
|
|
|
81 dev.off()
|
|
|
82 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
|
|
|
83 bar = as.matrix(foo)
|
|
|
84 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
|
|
|
85 heatmap(bar,main='Random Heatmap')
|
|
|
86 dev.off()
|
|
|
87 }
|
|
|
88
|
|
|
89 ]]></help>
|
|
|
90 <citations>
|
|
|
91 <citation type="doi">10.1093/bioinformatics/bts573</citation>
|
|
|
92 </citations>
|
|
|
93 </tool>
|
|
|
94
|
