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When running a complex workflow from the command line, is there a way to specify options for individual analysis tools (like within a cycle)? Otherwise, you would have to open up the workflow on the web, set the variables, and then launch it from the command line. Not ideal.

You should make all analysis parameters accessible from the outside as workflow parameters (those five-cornered boxes). It's possible for analyses inside cycles as well (though you have to put the workflow parameter outside of the cycle). After that you can set them via command line tool.

The "bind property to variable" seems to work fine. To expand on that, some of our analysis method options are drop-down lists and I see that the "green box" has two parameters "drop-down options" and "options expression". Is there a way to link them so that they use the same options? In most cases it's not a big deal because there's only a few options, but we have at least one "species" variable that has 30 or so pre-defined options.

There's an '(auto)' option in "drop-down options" select box. When you bind property and set this '(auto)' option, it tries to fetch list of options from bound analysis method. It works in the most of cases. You don't have to specify 'options expression' in this case.