Hi Jen,
Thanks again.

Just to make it clear: if all the options are not present on galaxy but only 
some of them, does this mean that the absent ones have been set by galaxy dev? 
are these to be considered best settings not worth changing? I would like to 
learn a bit more and "play" with all options but if some of them wont affect 
the final reaults then is not worth changing them.

Thanks,
Irene

From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: 14 November 2013 21:43
To: galaxy-user
Cc: Irene Bassano
Subject: Tophat/Cuff parameters

Hello,

Yes, this is correct, not all parameters can be adjusted in the UI. Many can, 
especially with Tophat, but not all. The list of implemented parameters that 
will match the documentation is listed at the bottom of each of these tools. 
The UI form itself up top may have a slightly different human readable name, 
but most will include the parameter name "-r", etc.

To see all of the parameters on the forms:
1. Tophat/2 - open "TopHat settings to use: Full parameter list"
2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full 
content

This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had 
programming resource available, then these could certainly be modified. 
Development questions can go do the 
galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu> mailing list, but really 
the best place to start is in our wiki:
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
http://wiki.galaxyproject.org/Tool%20Shed

It would be really helpful if you sent questions directly to the 
galaxy-u...@bx.psu.edu<mailto:galaxy-u...@bx.psu.edu> mailing list going 
forward.
Thanks,

Jen
Galaxy team

On 11/14/13 1:08 PM, Irene Bassano wrote:
> Hi Jen,
> thanks a lot for your reply.
>
> I am trying to apply some changes to certain parameters in cufflinks. I have 
> read them on the manual but on galaxy are not all listed.
> is this because they have been chosen already by galaxy and set to certain 
> values you guys believe are optimal?
> I cannot find for example:
>
> Maximum genomic length allowed for a given bundle.
> Minimum intron size allowed in genome.
> Minimum average coverage required to attempt 3' trimming.
>
> and many others.
>
> I also wanted to access full parameters for Tophat and Cuffdiff...
>
> Any suggestion on how can I access them?
>
> Thanks,
> Irene
--
Jennifer Hillman-Jackson
http://galaxyproject.org
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