A brief writeup of my experiences:
http://web.science.mq.edu.au/~cassidy/wordpress/2015/10/21/galaxy-tool-generating-datasets/
Steve
On 21 October 2015 at 18:27, Peter van Heusden wrote:
> These names have meaning in CollectedDatasetMatch:
>
> designation means designation if that exists else
These names have meaning in CollectedDatasetMatch:
designation means designation if that exists else name
name means name
dbkey means dbkey
ext means ext
visible means visible
On 21 October 2015 at 08:44, Steve Cassidy wrote:
> Thanks, yes that works, though I'm not really sure what the differ
Ah, thankyou, yes, I can now get results by using patterns to match the
output. I used your example but prepend 'simple' to the filename and then
searches for that with:
this solves the problem for the sample script but not generally since in
general I can't predict the filenames that will be ge
I poked around at your tool XML and the code a bit and the problem is
directory="$job_name". Galaxy expects to collect files from the job's
working directory - basically the current working directory the job runs
in. The directory= argument doesn't have variables expanded as far as I can
tell. In a
Yes, I'm sure that's where the problem lies. Writing out to the current
directory doesn't work. The files get written to
'job_working_directory/000/1/' but if I run the Upload File tool the result
is placed in 'files/000/'. I think I need to work out where to write the
files, I found some referen
I suspect that the problem might be in the then. I'm
not an export on this, but "__name_and_ext__" turns into the
regexp r"(?P.*)\.(?P[^\.]+)?" in
lib/galaxy/tools/parameters/output_collect.py, and is used by the
DatasetCollector (line 358). This looks like it should match the filenames
you're cre
Thanks Peter,
I did see that proviso somewhere but no, refreshing doesn't help.
That page was one of those that I referred to getting to this point.
Steve
On 20 October 2015 at 18:33, Peter van Heusden wrote:
> Just a quick check - did you refresh your history to confirm that the
> dataset *
Just a quick check - did you refresh your history to confirm that the
dataset *is* empty? We had the same thing at SANBI but it turns out that
Galaxy creates an empty output collection and then only populates it
sometime after job completion (this is a know UI bug).
See:
http://pvh.wp.sanbi.ac.za/
