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:jen@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:
- Tophat/2 - open "TopHat settings to use: Full parameter list"
- 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-dev@bx.psu.edu mailto:galaxy-dev@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-user@bx.psu.edu mailto:galaxy-user@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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