Cool extension to the growing feature set collectively known as "command line flowjo" (CLF), thanks to Jay. This specific feature will probably be included in the 7.6 series (we're still working out 7.5 'wrinkles').
The existing CLF switches in 7.5 allow users to create batches of flowjo analyses - which take arguments of template file and folder of data, and whether to quit, save, batch, whatever else - including creating file output like powerpoint batches or quicktime movies and excel spreadsheets. Neat.
In 7.6 Jay also added the ability to batch-export or batch-concat samples/gates..
This is really good news if you have 12Honkabyte files who need deflation into only those in gate B, but for 50 data sets. The type of stuff you can setup in a template and leave running overnight (data pre-processing ? )
From Jay's email:
It is now possible to perform the export/concatenate operation on a group, in addition to an individual population. This is performed by selecting the group and using the right button popup menu to 'Group Export/Concatenate...'. This opens the usual Export/Concatenate Dialog, but the operation will be performed on all samples in the selected group. You can also select a group-owned sub-population to perform this operation. When this dialog is opened, there is an additional checkbox in the dialog, to indicate whether you would like to save the export/concatenate operation with the template. If this checkbox is selected, then the template stores additional information to perform the export/concatenate operation when the template is opened using the command line invocation. It is hoped that this will provide the necessary functionality to build automated tests for the export/concatenate operation.
Here is how it works...
Create groups with ownership criteria so samples will be assigned to the groups automatically.
Create group-owned gates as needed.
In the Groups panel of the workspace, select a group-owned gate, popup the right button menu and choose 'Group Export/Concatenate...'.
Select the checkbox to 'Save with template'. Select 'Concatenate' if so desired.
Click the 'Export' button to perform the operation.
Perform multiple export/concatenate operations on different groups or subpopulations, as needed.
Now save the workspace as a template, and quit FlowJo.
Now start FlowJo using the command line, with two arguments: the full path and name of the template file (you should probably enclose the path with double quotes), and the full path and name of a folder of data files to load (again, encloses in double quotes).
After FlowJo loads the template, it will perform all export/concatenate commands, placing the newly created files in the same folder where the template is stored.
Feedback welcome...