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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