Appion

good point, I can do this today.

I recently added a file called stackPrepFormFrealign.inc which is where the new flag would be added.

We had originally hoped all preps would use the same parameters, but it seems we just can't keep it that way with frealign. So this new file inherits from stackPrepForm to get the basics.

You'll need to add a new param to the constructor, insert a field in the generateForm function and then make sure the command is generated correctly. Actually it looks like I'm already doing things with ctffindonly...might want to make sure we are not duplicating efforts.

Let me know if you have any ?'s regarding making the interface change, or if you just don't get to it today you can assign me a feature request.

updated the stackPrepFormFrealign.inc and prepRefineForm.php files to include the ctffindonly and paramonly options
r16309

Gabe,

How do you plan to use paramonly option? stack is added to files_to_remote_host in the function addStackToSend. If your stack for refinement is not in (or linked to) the recon directory at the end of prep in the same name, it will have an error in the actual running. Is it a concern?

I'm pretty sure that the "paramonly" option will be selected if the user is planning to run Frealign outside of Appion, so I wouldn't be concerned about this breaking subsequent steps.

Good to know. We have used the parameter output ourselves for exporting ctf values for outside users as well.