This syntax
*write.table(data1, file="{$out_data}", *
might not do what you expect. The $ has to be outside the braces, but
they're not needed there anyway - something like this might work better:
*write.table(data1, file="$out_data",..*
When things don't work, it's always useful to check the contents written
into that configfile script by setting job cleanup to never and taking a
look at the temporary folder noted in the galaxy log.
On Tue, Jun 24, 2014 at 2:35 AM, Jeremy Liu <jeremy....@yale.edu> wrote:
> Hi all,
>
> I have been trying to wrap a test r script into my local galaxy install
> using r_wrapper.sh but have been running with problems. When I run the
> tool, I get the following error in the side bar. For reference, I've pasted
> the xml file below.
>
> Error:
> Error in file(file, "rt") : cannot open the connection Calls: read.table
> -> file Error during wrapup: object 'l' not found Lost warning messages
> Execution halted
>
> The xml file:
> <tool id="r_script_test" name="Test R Script">
> <description>for proof of concept</description>
> <command interpreter="bash">r_wrapper.sh $script_file</command>
> <inputs>
> <param name="in_data" type="data" format="tabular" label="Test source
> file"/>
> </inputs>
> <outputs>
> <data name="out_data" format="tabular" />
> </outputs>
> <configfiles>
> <configfile name="script_file">
> ## Setup R error handling to go to stderr
> options(show.error.messages=F,
> error = function() { cat(geterrmessage(), file=stderr());
> q( "no", l, F)})
>
> ## Read in tab file
> data1 = read.table("{$in_data}", sep="\t")
>
> ## Output tab file
> write.table(data1, file="{$out_data}", quote=FALSE, sep="\t", eol =
> "\n", row.names=FALSE, col.names=FALSE)
>
> ## Close the session
> dev.off()
> </configfile>
> </configfiles>
>
> <help>
> This tools tests a R script to do simple file I/O
> </help>
>
> </tool>
>
> I have r_wrapper.sh copied in the same directory as the xml file. Any help
> would be appreciated!
>
> Thanks!
> Jeremy Liu
>
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