On Mon, Sep 30, 2013 at 7:07 AM, ruiwang.sz <ruiwang...@gmail.com> wrote:
> Hi Peter,
> Thanks! I got it working by putting a suppressMessages() around the function
> call.

Great, but what I meant was just add this to your XML file to tell Galaxy
to ignore the stderr and only use the return code for deciding if there
was an error. This way you get to see any warnings from your tool:

        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />

> I might have some questions on how to generate output file names on the
> fly...let me make some attempts
> first. :-)
> Best,
> Rui

Please read this thread first - there are already lots of people working on
wrapping deseq2 into Galaxy,

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