comparison rgToolFactory.xml @ 46:dbe3825e385c draft

Uploaded

45:7b34711416d2

output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
This can be handy for complex scripts creating lots of output.

**Examples**
<![CDATA[

Each of these following trivial examples can be cut and pasted into the script box for testing.
Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input

A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and 
writes the results to a new tabular file. Note the use of colClasses to ensure that no fiddling takes place with numeric values by treating everything

    pdf(paste('yet',i,"anotherheatmap.pdf",sep='_'))
    heatmap(bar,main='Random Heatmap')
    dev.off()
 }

A slight variation taking an input tabular file from which we read the first number as nreps

# note this script takes a single parameter
# number of replicates
ourargs = commandArgs(TRUE)
infname = ourargs[1]
nreps = read.table(infname,head=F)
nreps = unlist(nreps)[1]
nreps = max(c(1,nreps))
nreps = min(c(20,nreps))
print(paste("Using nreps=",nreps))
for (i in 1:nreps) {
   foo = runif(100)
   bar = rnorm(100)
   bar = foo + 0.2*bar
   pdf(paste("yet",i,"anotherplot.pdf",sep="_"))
   plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6)

   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("yet",i,"anotherheatmap.pdf",sep="_"))
   heatmap(bar,main="Random Heatmap")
   dev.off()
}

A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces 
for this to work if cut and pasted into the script box)::

 # reverse order of columns in a tabular file

 close(OF);
 close(NF);

]]>

**Citation**


Paper_ :

46:dbe3825e385c

output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
This can be handy for complex scripts creating lots of output.

**Examples**

<![CDATA[
Each of these following trivial examples can be cut and pasted into the script box for testing.
Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input

A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and 
writes the results to a new tabular file. Note the use of colClasses to ensure that no fiddling takes place with numeric values by treating everything

    pdf(paste('yet',i,"anotherheatmap.pdf",sep='_'))
    heatmap(bar,main='Random Heatmap')
    dev.off()
 }

A slight variation taking an input tabular file from which we read the first number as nreps::

 # note this script takes a single parameter
 # number of replicates
 ourargs = commandArgs(TRUE)
 infname = ourargs[1]
 nreps = read.table(infname,head=F)
 nreps = unlist(nreps)[1]
 nreps = max(c(1,nreps))
 nreps = min(c(20,nreps))
 print(paste("Using nreps=",nreps))
 for (i in 1:nreps) {
   foo = runif(100)
   bar = rnorm(100)
   bar = foo + 0.2*bar
   pdf(paste("yet",i,"anotherplot.pdf",sep="_"))
   plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6)

   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("yet",i,"anotherheatmap.pdf",sep="_"))
   heatmap(bar,main="Random Heatmap")
   dev.off()
 }

A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces 
for this to work if cut and pasted into the script box)::

 # reverse order of columns in a tabular file

 close(OF);
 close(NF);

]]>


**Citation**


Paper_ :