How can I get a txt output file from R
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") source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R") close(file) ... </configfile> </configfiles> <outputs><data format="txt" name="output.txt"/></outputs> ... </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
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/
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.
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 ___________________________________________________________ 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/
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 ___________________________________________________________ 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/
Surely not, but I had some doubts about this. No more. 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 ___________________________________________________________ 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/
Hi, I need one more help. The code that I cite before now is this: ... 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 filepdf=file("${relatorio}","w") ##I used this to declare an file to outputtexi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf = TRUE, clean = TRUE) ##generate the relatorio.pdf fileclose(pdf) ... <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 ___________________________________________________________ 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/
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?
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/
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.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
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?
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/
participants (3)
-
Bjoern Gruening -
Björn Grüning -
Ramon Tiburski