Ok, thanks a lot, I'll try and get back to the mailing list if other
problems seem to occur.
Pierre.
Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
http://abims.sb-roscoff.fr/
Le 30/01/2013 11:45, Ross a écrit :
I'd suggest:
1) Make your new datatype a subclass of Html - it's a subclass of
composite that contains an HTML document as the object's native
display - so it can inform users what's there.
2) When constructing these new things, pass the file_path of the Html
(composite) dataset subclass to your wrapper on the command line
3) Your wrapper code can construct any arbitrary structure as long as
it's rooted in that directory - Galaxy stores it without any fuss. The
wrapper should also populate the Html file itself with nicely
laid annotation for the user to check out.
4) The key is that all tools that take this new datatype as input must
know how to decode this structure - they must be passed the
$input.extra_files_path which gives them that same path root.
5) Yes, it's odd and annoying that it's extra_files_path for
files_path. Go figure.
6) grep extra_files tools/*.xml to find some examples - I think the
velvetg one uses a complex subdirectory structure - but it doesn't
really matter - as long as your tools know how to deal with it, it's
just a directory to Galaxy!
I hope all this helps...
On Wed, Jan 30, 2013 at 8:22 PM, Pierre Pericard
<pierre.peric...@sb-roscoff.fr <mailto:pierre.peric...@sb-roscoff.fr>>
wrote:
In that case, could anyone point me to an example of a Composite
Datatype which could accept as input an unknown number of files in
an unknown number of directories. I can't seem to understand how
that would work based on the wiki.
But maybe are we anticipating a near functionality of Galaxy.
There were talks about changing the way Galaxy handle zip files,
is it still on the table ?
Thank in advance for any help,
Pierre
Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
http://abims.sb-roscoff.fr/
Le 29/01/2013 18:04, Peter Cock a écrit :
On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard
<pierre.peric...@sb-roscoff.fr
<mailto:pierre.peric...@sb-roscoff.fr>> wrote:
If I'm not mistaking, Composite Datatypes allow for only
one directory,
whereas we need to keep a constant directory structure
with 2 or more
sub-directories containing our input files.
I'm not sure if that is true - the example of HTML output with
images
comes to mind as a common use-case where subfolder(s) would be
expected. I've only had limited first hand experience with
Galaxy's
composite datatypes myself though.
We have no way to change these tools behavior (obviously
not Galaxy-friendly
;-) ) and therefore need to maintain this structure in the
job working
directory.
Perhaps a tool wrapper could create a dummy folder using symlinks
(faster and less wasted disk than copying files), but that
isn't ideal.
Peter
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