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
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 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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