> Subject: Re: [galaxy-dev] How can I get a txt output file from R
> From: bjoern.gruening@pharmazie.uni-freiburg.de
> To: ramao_tiago_tiburski@hotmail.com
> CC: bjoern.gruening@gmail.com; galaxy-dev@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.gruening@gmail.com
> > > To: ramao_tiago_tiburski@hotmail.com
> > > CC: galaxy-dev@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.gruening@gmail.com
> > > > > To: ramao_tiago_tiburski@hotmail.com
> > > > > CC: galaxy-dev@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
> > > > > > ___________________________________________________________
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> >
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