On Fri, May 6, 2011 at 10:17 AM, SHAUN WEBB <swe...@staffmail.ed.ac.uk> wrote:
> Hi, I have created a tool that will fetch sequences for selected IDs from a
> tabular file containing multiple IDs and additional info.
> I want the tool config to scan the first column of the tab file for IDs and
> provide the user with a selection box where they can select a single ID or
> multiple IDs and get output for all selected.
> The following method does this:
> <param name="tabfile" type="data" format="tabular" label="ID File"/>
> <param name="selection" type="select" multiple="true" accept_default="true"
> label="ID" >
>              <options from_dataset="tabfile">
>                              <column name="name" index="0"/>
>                              <column name="value" index="0"/>
>              </options>
>  </param>
> The issue is, if the top file in my history is a SAM file containing ~30,000
> IDs in the first column the tool initially attempts to load these all in to
> the selection box and effectively crashes my local instance.
> I only want to use this on tab files that ill have ~100 IDs at most.

Maybe the <options from_dataset="tabfile"> tag could have a max
setting? e.g. <options from_dataset="tabfile" max="100"> could
load just the first 100 entries in the tabular file. That seems much
more general than the new filetype idea.

It could have a default max value which should useful.

Thinking of the example of a tabular file of gene IDs for an organism,
you might well want 20 to 30 thousand entries. Since Galaxy puts
a search function on the selection, the UI should be OK. Its just the
performance we need to worry about.


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