On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
> On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
>> Thank you for your quick response, my command tag is:
>> <command>
>> interpreter="bash">Rscript_wrapper.sh
>> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
>> $pathwayid $species $output
>> </command>
>> So I believe Im calling R via the Rscript_wrapper.sh?

There is a problem with the XML closing of the <command> tag.
You appear to have a bash script calling an R script. Try:

<command interpreter="bash">Rscript_wrapper.sh
$genedata $pathwayid $species $output

Or, if you mark your shell script as executable and include
the #!/bin/bash line, you don't need the interpreter setting:

$genedata $pathwayid $species $output

Also, you should be able to use relative paths rather than
that absolute path (which is not portable).

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