Hello Jianguang,
Setting the type during loading from the FTP area into a history as a
dataset is optional. Through experience, I believe that this helps to
speed up the process, but this is purely anecdotal.
For datasets that have been imported, but have not had format
auto-detected, or the format detected was incorrect or not specific
enough (e.g. "fastq" when you want "fastqsanger"), just edit the
dataset's attributes. Click on the pencil icon in the upper right corner
of any dataset, click on the dataset tab in the form that comes up in
the middle panel, pick the type from the menu, and save.
This can be done with any dataset, at any point. After running certain
tools, reassignment of datatype or other metadata (column assignments,
found on the first tab of the same "Edit Attributes" form above) is
needed - often the tool will note if this is the case.
Galaxy has some logic that will prevent the misalignment of obviously
incorrect metadata - including widely inappropriate datatypes. But
tuning the type to be specific and correct between a group of common
format datatypes (for example: a group like "tabular, bed, interval")
would be for you to ensure.
Setting "database" is also optional and can be performed during or after
loading, or at any other time, by clicking through the pencil icon on
Edit Attributes form (first tab).
In most cases - skip converting spaces to tabs - unless you really are
working with a strict tabular dataset and are certain that no fields
contain internal whitespace (including informative/metadata headers).
Hopefully this helps,
Jen
Galaxy team
On 3/21/13 7:30 AM, Du, Jianguang wrote:
Hi Everyone,
When I upload my datasets onto my history via FTP method (using
FileZilla), do I need to specify the file format under "File Format"
of "Upload File from your computer"?
I noticed that the screencast of how to upload datasets via FTP just
leaves the "File Format" as "Auto-detect". However, I also noticed
this sentence in the help for Auto-detect: "the system will attempt to
detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular,
Wiggle, Bed and Interval (Bed with headers) formats". Do I need to
specify the format of my datasets if the format of my datasets is not
listed in the sentence above?
Thanks.
Jianguang
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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