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view toolfactory/tfout/plotter.xml @ 4:2a46da701dde draft
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author | fubar |
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date | Mon, 26 Apr 2021 05:25:26 +0000 |
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<tool name="plotter" id="plotter" version="0.01"> <!--Source in git at: https://github.com/fubar2/toolfactory--> <!--Created by planemo@galaxyproject.org at 31/03/2021 10:58:49 using the Galaxy Tool Factory.--> <description>Makes random plots</description> <requirements> <requirement version="" type="package">r-base</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <expand macro="stdio"/> <version_command><![CDATA[echo "0.01"]]></version_command> <command><![CDATA[Rscript $runme "$nplot"]]></command> <configfiles> <configfile name="runme"><![CDATA[ \# demo args = commandArgs(trailingOnly=TRUE) if (length(args)==0) { n_plots = 3 } else { n_plots = as.integer(args[1]) } dir.create('plots') for (i in 1:n_plots) { foo = runif(100) bar = rnorm(100) bar = foo + 0.05*bar pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_')) plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6) dev.off() foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) bar = as.matrix(foo) pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_')) heatmap(bar,main='Random Heatmap') dev.off() } ]]></configfile> </configfiles> <inputs> <param name="nplot" type="text" value="3" label="Number of random plots pairs to draw" help=""/> </inputs> <outputs> <collection name="plots" type="list" label="Plots"> <discover_datasets pattern="__name_and_ext__" directory="plots" visible="false"/> </collection> </outputs> <tests> <test> <param name="nplot" value="3"/> <output_collection name="plots"/> </test> </tests> <help><![CDATA[ **What it Does** Makes plots into a collection demonstration ------ Script:: # demo args = commandArgs(trailingOnly=TRUE) if (length(args)==0) { n_plots = 3 } else { n_plots = as.integer(args[1]) } dir.create('plots') for (i in 1:n_plots) { foo = runif(100) bar = rnorm(100) bar = foo + 0.05*bar pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_')) plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6) dev.off() foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) bar = as.matrix(foo) pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_')) heatmap(bar,main='Random Heatmap') dev.off() } ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/bts573</citation> </citations> </tool>