i wanted to post about something i found out today working with the MACS tool (under NGS: peak calling) for ChIP analysis. i found that the MACS tool will run with the 'use fixed background lambda as local lambda for every peak region' box invisibly checked when used as part of an automated workflow. you will see an error message in the MACS html output file that says !!!! DYNAMIC LAMBDA IS DISABLED !!!!. the results appear incorrect as well.
this is a bug, but you can get around it by checking this option box in the saved workflow - this has the effect of running as unchecked.
i can't find the bug report button, so i haven't reported it as a bug, but it would be good to fix probably. perhaps there are other invisibly checked options with this tool as well that i haven't noticed.
p.s. i am using the online interface for Galaxy at galaxyproject.org