search

kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
64 stars 19 forks source link

Is is possible to do quality control and parse at the same time? #33

Closed sorenwacker closed 5 years ago

sorenwacker commented 5 years ago

It seems the commandline arguments for qc and parse are somewhat mixed. So essentially, one has to run rawtools parse and rawtools qc as separate commands. Is that correct? I also wonder, for quality control if files are continuously added to the same directory? Would rawtools recognise which files it has already processed or would it process all files again. The qc module has no -f option only -d.

kevinkovalchik commented 5 years ago

We are planning to allow parse and qc at the same time. You can actually do this with the GUI beta. We haven't streamlined it yet, but if you download that version you can do it. I imagine you will be using the CLI, so just run RawTools.exe from the GUI release rather than RawToolsGUI.exe. To do both, use this syntax: RawTools.exe all -d [directory] -q [QC directory] {other options from QC or parse} I believe that is how it was set up. The "all" verb is a bit clunky, so I'll clean up the interface more at some point. Also, if you set up an analysis in the GUI using g both QC and parse and start it, the command line arguments will be saved in the log file, so you can check out how to do it in there if my above suggestion doesn't seem to work. Note the GUI version is built on 1.4.1, so any bugs that have been fixed since then will still be there.

For your second question, yes it will only process new files that get added. So if you run it on 10 files, then add one more to the directory and run the program again it will only process that one file and add the data to the QC files.

Kevin

On Wed, Feb 20, 2019, 12:48 PM Sören notifications@github.com wrote:

It seems the commandline arguments for qc and parse are somewhat mixed. So essentially, one has to run rawtools parse and rawtools qc as separate commands. Is that correct? I also wonder, for quality control if files are continuously added to the same directory? Would rawtools recognise which files it has already processed or would it process all files again. The qc module has no -f option only -d.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kevinkovalchik/RawTools/issues/33, or mute the thread https://github.com/notifications/unsubscribe-auth/APT50NkiuSAmLNfVyJiDCYspscqg_T5Fks5vPbSigaJpZM4bGFbp .