Hello -
Most of these are at defaults. The source code is the best place to find
any that are hard-coded (if included, most likely done to manage
resources). Again, any of of this could be modified if you have
programming resource. The repository is owned by the devteam and in the
Tool Shed, search with "cuff" here: http://usegalaxy.org/toolshed
Best,
Jen
Galaxy team
On 11/15/13 2:59 AM, Irene Bassano wrote:
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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--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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