Hi Galaxy team: I am interested in analysis RNA-seq of repetitive elements and optimal alignment setting includes adjusting --winAnchorMultimapNmax (under "Windows, Anchors, Binning" section) parameter in STAR tool. But I am unable to adjust this parameter in the panel. Is it possible to add this to the tool panel? Thanks!
This option is left at the default (50) in the current Galaxy wrapped version of the tool. Changing this option can impact runtime significantly, and interacts with other settings (many of which are also not end-user configurable). This parameter and related parameters used in certain combinations along with the content of data inputs can create jobs that will never complete, which is probably why it is not included.
If you want to test out this parameter (and others not end-user adjustable), you could modify the tool wrapper and install it on your own Galaxy server. Alternatively, if you want to double check with the developers about adding this option to the existing tool wrapper, either open an enhancement request ticket at the development repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar or contact the IUC team directly at their Gitter channel to see what they think about this change first https://gitter.im/galaxy-iuc/iuc.
Help when using Planemo for tool development:
Thanks! Jen, Galaxy team