Batch run mode

[mwang87]

Is it possible to classify features just on the commandline in linux rather than the GUI?

[macraild]

Not officially.

But this script https://github.com/macraild/peakonly/blob/master/peakonly_batch.py reimplements a simplified version of processing_utils.runner.FilesRunner._batch_run, to give access to the basic functionality from the command line. Its an ugly hack, but in my hands gives identical results to the GUI.

Minimally,
python peakonly_batch.py --mzML *.mzML
should work as long as the peakonly install dir is on your PYTHON_PATH, but check
python peakonly_batch.py -h
for other options.

[sorenwacker]

I get:

python peakonly_batch.py --mzML /data/Metabolomics/MS-formats/MTBLS1569/mzML/QC_*

peakonly_batch.py [-h] [--mzML mzMLfiles] [--mz-deviation MZ_DEVIATION] [--min-ROI-length MIN_ROI_LENGTH] [--max-zeros MAX_ZEROS] [--min-peak-length MIN_PEAK_LENGTH]
[--model-dir directory] [--csv csvFiles] [--png directory]
peakonly_batch.py: error: unrecognized arguments: /data/Metabolomics/MS-formats/MTBLS1569/mzML/QC_1.mzML /data/Metabolomics/MS-formats/MTBLS1569/mzML/QC_2.mzML /data/Metabolomics/MS-formats/MTBLS1569/mzML/QC_3.mzML /data/Metabolomics/MS-formats/MTBLS1569/mzML/QC_4.mzML

[macraild]

Yes, I forgot that *nix and Windows handle command-line wildcards differently.
I've updated the script to fix.