Hi Saket
If you want to redirect the executable's stdout to a new Galaxy dataset
you've defined as $output, something like:
> '$output'
is a workable idiom for a command line AFAIK - you need to escape the
redirection '>' character or you'll confuse the xml parser.
It's often possible to hack a complex command line (or use configfile to
write a script!) but as Peter says, it all boils down to personal
preference - they all work.
Use whatever you find most convenient but remember you may need to maintain
it :)

On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <sake...@gmail.com>
> wrote:
> > As part of a warmup, I added a tool for perming eQTL analysis using
> > PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
> >
> >
> > By default PANAMA writes to stderr and creates a PANAM_results.csv file
> in
> > the same directory as the input files.
> >
> > I wrote ... XML : https://gist.github.com/saketkc/5697388
> >
> > Apparently the above XML runs too, but I dont get back a CSV.
> Essentially I
> > need to move the PANAMA_results.csv file to output1. Can this be done
> > without using a  wrapper at all , just using the XML files ?
> >
> > Is there a way to nest the commands in the XML so that I could do a
> > <move command> after <panama command> , but how would the paths be
> specified
> > ?
> Hi Saket,
> You could try this (two commands in one shell line), but catching error
> conditions would be a problem:
> <command>panama $expression_data $snp_data; mv PANAMA_results.csv
> $output1</command>
> In cases like this where the underlying tool is too inflexible to accept an
> output filename, I would personally use a wrapper script which can handle
> moving things to the desired location, and raising a clear error if the
> file
> was not created.
> Peter
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