Anthony,

We had some discussion on the galaxy dev list about R. See for instance my posting of Oct 14^th and several others as well (for ref sake a snippet is attached below).

That example opens an R script outside tool config (in this case a script that opens an input file and generates some output file which is grabbed by galaxy).

Hope this helps,

Alex

   <command>

         R –slave --vanilla -f $in_r --args $in_data $out_data

   </command>

   <inputs>

       <param name="in_data" type="data" format="tabular" label="Test data file" />

       <param name="in_r" type="data" format="text" label="R script to load and execute" />

   </inputs>

   <outputs>

       <data name="out_data" type="data" format="tabular" label="R script output" />

   </outputs>

The R script provided will grab the args from the cmd line as you indiciated earlier:

    # R script file to grab input and output filenames from cmdline and just copy

    args <- commandArgs()

    output <- read.table(args[6], header=T)

    write.table(output,sep="\t",file=args[7],row.names=F)

    #end script

Van: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] Namens Anthony Ferrari
Verzonden: dinsdag 9 november 2010 15:21
Aan: galaxy-user@lists.bx.psu.edu
Onderwerp: [galaxy-user] plugging R into galaxy

Dear galaxy users,

My team is involved in the NGS field. We have our own local cluster and we are looking for a workflow management system. Currently we are trying to set up and test galaxy. 

For our quality control analysis pipeline, R statistical software will be used. So we want to be able to call R scripts from galaxy.

I know that it is possible and the xy_plot.xml is a really good example (conditional & when, repeat  tags). Also, in this example a <configfile> tag is used. Within this tag you put your R code. And moreover you can add lines beginning with only one '#' which will be interpreted with cheetah template engine. This is helpful to create dynamic content of your R code with respect to your submitted parameters. (an old screencast introduces this example)

My question is : is there a way to avoid the <configfile> section and to let all the R code be outside the tool's xml config file? If yes, how can we specify an output file in the xml conf that will catch, for instance, a write.table() call in the R script ?

Best regards,

Anthony