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-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 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