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.liu@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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