Question: Limiting blast output on the Cloud
1
gravatar for avoltz
20 months ago by
avoltz30
avoltz30 wrote:

I'm using galaxy on the cloud. Is there a way to limit blast output? For example, when I run command line blast I can use "max_target_seqs" to limit the output. I don't see this choice anywhere in the documentation. Does anyone know if there is a way to set something so I don't get so many blast hits per query? Thanks, Amy

filters parameters blast cloud • 516 views
ADD COMMENTlink modified 20 months ago by Bjoern Gruening5.0k • written 20 months ago by avoltz30

Which Galaxy Blast wrapper are you using? You can include a link to the Tool Shed, the tool version reported on the "i" Info form (included per dataset), or anything that specifies a particular tool/wrapper that can be found uniquely in the Tool Shed http://usegalaxy.org/toolshed. Jen, Galaxy team

ADD REPLYlink written 20 months ago by Jennifer Hillman Jackson25k

Hi Jennifer, How would I know which Blast wrapper I am using?

Amy

ADD REPLYlink written 20 months ago by avoltz30

This is noted as part of the tool name as displayed in Galaxy. The upper "Options" menu also has a link-out to the Tool Shed repository the tool was sourced from - and this has the full exact version name.

The Tool Shed will also have the repository tip files which can be used to map out which command-line options are supported on the tool form. You might be able to look at these yourself - create an account on the Tool Shed (http://usegalaxy.org/toolshed). log in, navigate to the too, and use the "Repository Actions" menu.

Or, I'll be able to help more and point you to the option (if supported) if I know which tool version you are using. Different versions/tool authors may structure the tool form differently.

Next time please reply as a comment so that this stays open until we are able to resolve the question. :) thanks!

ADD REPLYlink modified 20 months ago • written 20 months ago by Jennifer Hillman Jackson25k
0
gravatar for Bjoern Gruening
20 months ago by
Bjoern Gruening5.0k
Germany
Bjoern Gruening5.0k wrote:

Hi,

please look for an option that is called Maximum hits to show. This should do the trick.

Ciao, Bjoern

ADD COMMENTlink written 20 months ago by Bjoern Gruening5.0k
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