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/
> > > > 
> > > > 
> > > > 
> > > 
> > 
> > 
> > 
> 



___________________________________________________________
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/

Reply via email to