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Expert Review - Thermo diogobor  2025-11-19 06:54
 

Hello,

I'm trying to run Expert Review external tool from Thermo via CLI (command line), but I'm not able to get the results and send back to skyline in order to obtain the correct integrated peaks.

The external tool works pretty well on the graphical interface. Is there a way to run it via command line ?

I tried to use:
--tool-add="Thermo\Expert Review" ^
--tool-conflict-resolution="overwrite" ^
--tool-program-macro="ExpertReview,1.0" ^
--tool-program-path="C:\Users\workstat\AppData\Local\Apps\2.0\CWMKAT46.3P7\60MOKXQP.7YG\skyl..tion_9286511f3362df93_0019.0001_e71402c3ddc399fe\Tools\Sky3432\Thermo.TNG.PeakPick.SkylineTool.exe" ^
--tool-initial-dir="C:\Users\workstat\AppData\Local\Apps\2.0\CWMKAT46.3P7\60MOKXQP.7YG\skyl..tion_9286511f3362df93_0019.0001_e71402c3ddc399fe\Tools\Sky3432" ^
--tool-command="$(ToolDir)\Thermo.TNG.PeakPick.SkylineTool.exe" ^
--tool-arguments="$(DocumentPath)" $(SkylineConnection) "$(InputReportTempPath)" ^
--tool-report="Thermo_ART_Integration" ^

but it didn't run the tool.

Thanks in advance.
 
 
philip remes responded:  2025-11-19 09:55

Hi Diogobor,

The tool as installed in Skyline can't be run from the command line. But it is possible is to give you a version of the Skyline tool that has a Thermo.TNG.PeakPick.Console.exe in it. You would be able to navigate to where Skyline installs the tool and open a command window or in other code make a call to Thermo.TNG.PeakPick.Console.exe path_to_json_config file. You would be able to get a template of the json config file by running Expert Review once from the User interface and looking at the ./art_peaks/parameters.json file that's produced after it runs. What this file specifies is mainly the paths to Skyline reports used by Expert Review. It could be a little unwieldy by itself though because you need to create those reports. So, I have some Python code that calls the Skyline API to export the report that Expert Review needs, then run Expert Review and import those boundaries back to Skyline.

If this sounds interesting, you can send me an email at philip.remes@thermofisher.com, I can give you this version of the Skyline tool and share the Python code, and we can see if this is what you are looking for.

Thanks
Philip