CLI options

raw2mzDB options:

Convert a rawfile into mzDB file

User can decide to centroidize or fit certain ms level. If available, centroidization are performed using vendor algorithms. Otherwise, 2 peak pickers are used depending of the rawfile:

• Thermo: custom peak picker
• Others: pwiz continuous wavelet transform

Generally, options have short and long term which is followed by value or not. Short term are preceded by -, longer terms by --.

-i, --input : specify the input rawfile path
-o, --output : specify the output filename (must be an absolute path)
-c, --centroid : centroidization, eg: -c 1 (centroidization msLevel 1) or -c 1-5 (centroidization msLevel 1 to msLevel 5)
-p, --profile : idem but for profile mode
-f, --fitted : idem buf for fitted mode
-T, --bbTimeWidth : bounding box width for ms1 in seconds, default: 15s
-t, --bbTimeWidthMSn : bounding box width for ms > 1 in seconds, default: 0s
-M, --bbMzWidth : bounding box height for ms1 in Da, default: 5Da
-m, --bbMzWidthMSn : bounding box height for msn in Da, default: 10000Da
--dia : will force the conversion in DIA mode"
--no_loss : if present, leads to 64 bits conversion of mz and intenstites (larger ouput file)
--nscans : nb scans to convert into the mzDB file (max: number of scans in the rawfile)
-h --help : show help