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Topic: Possible to export MSDIAL alignment results from console app? (Read 298 times) previous topic - next topic

Possible to export MSDIAL alignment results from console app?

Hi all,
    I'm wondering if it's possible to export MSDIAL alignment results using the console application (or other script!). I'm currently using it as a kind of semi-targeted method where I run it but then go back and modify the peak boundaries for those features I know are problematic and for which I need high-quality data. I'd like to then script the export of that peak list rather than needing to go through the point-and-click process of exporting the results to a text file manually, and it seems like this is something the console app could do? Specifically, I'd like to open an existing .mtd2 file, click the "Export" tab, select "Alignment result", specify the output directory, check a couple of the boxes, change the output format to text, and hit the "Export" button at the bottom. Is this possible or planned to be included in a future update? Or does the console app only do truly hands-off untargeted processes?
    -Will

Re: Possible to export MSDIAL alignment results from console app?

Reply #1
I have been trying to figure this out for so long!!! This would be VERY helpful. As far as I can tell, all uses of the console application require GUI application as well. For many situations, it would be nice to be able to get results without opening the GUI. Exporting results tables would allow for a full analysis with the console application, but it would also be nice to be able to perform ion amalgamation, RT correction, and other MS-DIAL functions from the command line.

Re: Possible to export MSDIAL alignment results from console app?

Reply #2
Bumping this up again to see if anyone knows whether this is possible or likely to be added as a feature! Still of major interest to me for creating a reproducible workflow with MSDIAL