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. Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
