This option is available under "Advanced settings" as the option "Maximum genomic length of a given bundle" with a default of "3,500,000bp", listed as a configurable option on the tool form, when advanced settings are implemented. These are not implimented on the Cufflinks version offerered on the free public Main Galaxy server at http://usegalaxy.org, but it can be set to be active after the Cufflinks repository is installed from the Main Tool Shed at http://usegalaxy.org/toolshed into a local or cloud Galaxy.
Adjusting this option will consume much more resource, which is why the version on the Main server is configured without this option. This is necessary to permit all researchers to use the public resource in a fair way. No project can support all versions/options of compute intensive tools/jobs, even with considerable resources (the Main instance is for all users, world-wide, and has very significant dedicated resources).
That said, Galaxy is free and easy to set up for your own use. A researcher using their own server (local or cloud) can experiment with the option by allocating more dedicated resource. The tool uses the same resources whether run line-command or within Galaxy once the job is launched, so if it works on your platform of choice command-line, with the given resources, it will also work within Galaxy if installed on the same system. (All 3rd party tools/binaries wrapped in Galaxy utilize resources this way).
If this interests you, I can share a few links to help you get set started:
- Galaxy itself is free! Always.
- Choices about where to use Galaxy, including a matrix of the types of jobs/projects vs the best platform are in this wiki: https://wiki.galaxyproject.org/BigPicture/Choices
- It is commonly believed that using a cloud (aka "Cloudman") Galaxy is prohibitively expensive to use by researchers. But this is absolutely not true. AWS offers generous grants (see: http://aws.amazon.com/education/aws-in-education-research-grants/). Plus the cloud has the advantage of being much easier to set up and administer temporary resource on demand (through a GUI).
- Cufflinks (and all other Galaxy tools not included in the primary release) are in the Tool Shed. Review the Cufflinks repository here: https://toolshed.g2.bx.psu.edu/view/devteam/cufflinks
- If you login into the Tool Shed, the repository tip files can be viewed online. This is where one can quickly review implemented options in the .py and .xml (both include the "--max-bundle-frags" option for this tool).
You may have found an alternate solution by now, but this seemed worth sharing. Best, Jen, Galaxy team