comparison toolfactory/tfout/plotter.xml @ 4:2a46da701dde draft

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4:2a46da701dde

<tool name="plotter" id="plotter" version="0.01">
  <!--Source in git at: https://github.com/fubar2/toolfactory-->
  <!--Created by [e-mail] 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>