The previous code doesn't work in the command line, but this yes:

file=file("output.txt","w")source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")close(file)
Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw")
pdf=file("relatorio.pdf","w")  ## I changed here
texi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf = TRUE, 
clean = TRUE) 
This code works in the command line, but I didn't use this because of 
"pdf=file("relatorio.pdf","w")", the problem is that if I use this code on 
Galaxy, it don't recognizes my pdf output. In fact, my code creates an pdf 
file, and my intention is override it with the last command, but to do this I 
need that the name declared in Galaxy be the same of the generated by the 
function, that is "relatorio.pdf". Do you understand me?
Thank you
> Subject: Re: [galaxy-dev] How can I get a txt output file from R
> From: bjoern.gruen...@pharmazie.uni-freiburg.de
> To: ramao_tiago_tibur...@hotmail.com
> CC: bjoern.gruen...@gmail.com; galaxy-...@bx.psu.edu
> Date: Mon, 30 Sep 2013 23:03:34 +0200
> 
> Hi,
> 
> > 
> > 
> > 
> > file=file("output.txt","w")
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > close(file)
> > 
> > Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw")
> >  ##generate the relatorio.tex file based on the output.txt file
> > 
> > pdf=file("${relatorio}","w")  ##I used this to declare an file to
> > output
> > 
> > texi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf =
> > TRUE, clean = TRUE)   ##generate the relatorio.pdf file
> > 
> > close(pdf)
> 
> 
> I can't see any obvious error. Is the R code correct if you test it on
> commandline? Also please use a $tmp file path and clean up afterwards. I
> can imagine, that output.txt is not found by Sweave.
> 
> > 
> > ...
> > 
> > <outputs>
> > <data format="pdf" name="relatorio"/>
> > </outputs>
> > 
> > Now I want to write the txt file (output.txt) to a pdf file using
> > Latex (Sweave), so the function "Sweave" generate the file
> > "relatorio.tex" e this is used by the function "texi2dvi" to generate
> > the pdf file, but it is generate with the name "relatorio.pdf" and I
> > don't know what to do, because with the code above I get an empty pdf
> > file. What can I do?
> > 
> > 
> > Thank you
> > 
> > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > From: bjoern.gruen...@gmail.com
> > > To: ramao_tiago_tibur...@hotmail.com
> > > CC: galaxy-...@bx.psu.edu
> > > Date: Mon, 30 Sep 2013 20:01:41 +0200
> > > 
> > > Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski:
> > > > Thank you, you solved my problem. Maybe you can help with one more
> > > > thing, Can I interact in the middle of an workflow execution ? For
> > > > example: I have a workflow with ten steps and after I started
> > this, I
> > > > want to select options always before each step (like a software
> > > > instalation). Is it possible? Thank you one more time.
> > > 
> > > I don't think that is possible. Is that still a workflow?
> > > 
> > > Ciao,
> > > Bjoern
> > > 
> > > > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > > > From: bjoern.gruen...@gmail.com
> > > > > To: ramao_tiago_tibur...@hotmail.com
> > > > > CC: galaxy-...@bx.psu.edu
> > > > > Date: Mon, 30 Sep 2013 19:18:55 +0200
> > > > > 
> > > > > Hi Ramon,
> > > > > 
> > > > > 
> > > > > > Code:
> > > > > >
> > ________________________________________________________________
> > > > > > <tool id="predictionModelTool" name="Modelo de Deteccao de
> > Risco">
> > > > > > ...
> > > > > > <command interpreter="bash">r_wrapper.sh
> > $script_file</command>
> > > > > > <inputs>
> > > > > > ...
> > > > > > </inputs>
> > > > > > <configfiles>
> > > > > > <configfile name="script_file">
> > > > > > 
> > > > > > ...
> > > > > > 
> > > > > > file=file("output.txt","w")
> > > > > 
> > > > > Do not hardcode a filepath here, you need to reference the
> > template
> > > > > variable from your output section (name="output").
> > > > > 
> > > > > For example:
> > > > > file=file("${output}","w")
> > > > > 
> > > > > >
> > > >
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > > > > > close(file)
> > > > > > 
> > > > > > 
> > > > > > ...
> > > > > > 
> > > > > > </configfile>
> > > > > > </configfiles>
> > > > > > 
> > > > > > <outputs><data format="txt" name="output.txt"/></outputs>
> > > > > 
> > > > > and here change that to:
> > > > > <outputs><data format="txt" name="output"/></outputs>
> > > > > 
> > > > > 
> > > > > Cheers,
> > > > > Bjoern
> > > > > > 
> > > > > > ...
> > > > > > </tool>
> > > > > >
> > ________________________________________________________________
> > > > > > 
> > > > > > 
> > > > > > I'm having the output "empty" and I need that the result be
> > > > generated
> > > > > > in a text file. What can I do?
> > > > > > 
> > > > > > 
> > > > > > Thank you
> > > > > > ___________________________________________________________
> > > > > > 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/
> > > > > > 
> > > > > > To search Galaxy mailing lists use the unified search at:
> > > > > > http://galaxyproject.org/search/mailinglists/
> > > > > 
> > > > > 
> > > > > 
> > > > 
> > > 
> > > 
> > > 
> > 
> 
> 
> 
                                          
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