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
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
Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski: 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?
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