The first example should now work - maybe your variant of Galaxy was
to old at the time? I added that at the request of Michael Crusoe
during the last virtual contribution fest.
https://github.com/galaxyproject/galaxy/commit/07dd69edd5472afef305fb170f18628a0cf3402d
Otherwise, using ext instead
Hi all,
I have a related issue as I'm trying to set the format on discovered
datasets. Only setting e.g 'ext="fastqsanger"' seems to work. But the
following variations do not work to set a format, and similar to Alexander,
the history items do not show any datatype with these options.
no - not a typo. The tool can process both.
It's just my naming, because I use it for fastq.
I'll change the help tag.
2015-06-25 3:44 GMT-05:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Alexander,
If this wasn't a collection, I would expect format_source to work
(possibly also using
Hi John,
yes - I created this hacky solution and it works.
I now tried what you said, but no success.
Code:
collection name=split_output type=list label=@OUTPUT_NAME_PREFIX@
on ${on_string} (Fastq Collection) format_source=fastq_input1
discover_datasets
You are giving Galaxy mixed signals :). format_source will say to use
the data type specified by the corresponding input - but
discover_datasets pattern=__name_and_ext__ directory=splits /
Is saying (with the pattern __name_and_ext__) read files of the form
out1.fastq and assign the collection
