Carlos, You'll want to have your wrapper collect output to stderr and report only if the tool fails. See the Cufflinks/compare/diff wrappers for examples of how this can be done. Good luck, J. On Jan 30, 2012, at 1:01 PM, Carlos Borroto wrote: > Hi all, > > I'm working on integrating cummeRbund[1] into Galaxy. This is a very > helpful tool for analysis and visualization of cuffdiff output. > > My problem is any text output from running R code, puts the galaxy > output in error state. Even if everything is working correctly and the > outputs are generated as intended. I tried this code from > 'tools/plotting/xy_plot.xml': > ## Setup R error handling to go to stderr > options( show.error.messages=F, >    error = function () { cat( geterrmessage(), file=stderr() ); q( > "no", 1, F ) } ) > > But it didn't help. Even for loading the library I had to go with: > suppressPackageStartupMessages(library("cummeRbund")) > > Nothing else would work. Now the tool is outputting some messages > while running R functions, which is putting the output in galaxy in > error state. I'm thinking about asking the upstream developer to > provide a way to run the functions in the library in 'quite' mode. Is > there any other option? > > Right now I'm using the path of creating a R script in the XML file > and using r_wrapper.sh to run it. I tried first with rpy, as it would > give me more freedom, but cummeRbund use ggplot2 which seems to be > supported only on rpy2. > > [1]http://compbio.mit.edu/cummeRbund/ > > Thanks in advance, > Carlos > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client.  To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > >  http://lists.bx.psu.edu/