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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