singjust/openmsscripts repository overview

$ docker run -it --rm -v `pwd`:/data/ singjust/openmsscripts:latest openswathworkflow_calibration_report --help
Name: 
        Generate calibration reports for m/z, iob mobility and retention time using debugging files from OpenSwathWorkflow

    Usage: 
        Rscript openswathworkflow_calibration_report.R --[args] | --help

        Example: Rscript openswathworkflow_calibration_report.R --wd=./ --im_cal_pattern=_debug_im.txt --mz_cal_pattern=_debug_mz.txt --irt_trafo_pattern=.trafoXML --irt_mzml_pattern=_irt_chrom.mzML --report_file=calibration_report.pdf --zoom_in_xic=TRUE


    Options: 
        --wd: File path to OpenSwathWorkflow debugging files. Default: current working directory
        --im_cal_pattern: Pattern that identifies the ion mobility debugging file. Default: _debug_im.txt
        --mz_cal_pattern: Pattern that identifies the m/z debugging file. Default: _debug_mz.txt
        --irt_trafo_pattern: Pattern that identifies the iRT transofrmation debugging file. Default: .trafoXML
        --irt_mzml_pattern: Pattern that identifies the iRT extracted ion chromatogram debugging file. Default: _irt_chrom.mzML
        --report_file: The output report file to save plots to. Default: calibration_report.pdf
        --zoom_in_xic: Zoom into the iRT XICs based on the identified RT apex from the trafoXML file. Default: TRUE
        --verbose: Print verbose information to the console. One of 0,1,2 for different levels of verbosity. Default: 0
        --help: Display this help message