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"The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
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v =>parseInput.OutputDirectory=v
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},
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{
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"b=|output_file",
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"b=|output=",
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"The output file. Specify this or an output directory -o. Specifying neither writes to the input directory.",
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v =>parseInput.OutputFile=v
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},
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{
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"o=|output_directory=",
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"The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
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v =>parseInput.OutputDirectory=v
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},
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{
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"s|stdout",
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"Write to standard output. Cannot be combined with file or directory output. Implies silent logging, i.e. logging level 0",
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v =>parseInput.StdOut=v!=null
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},
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{
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"f=|format=",
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"The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet; both numeric and text (case insensitive) value recognized. Defaults to indexed mzML if no format is specified.",
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"The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for None (no output); both numeric and text (case insensitive) value recognized. Defaults to indexed mzML if no format is specified.",
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v =>outputFormatString=v
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},
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{
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"m=|metadata=","The metadata output format: 0 for JSON, 1 for TXT; both numeric and text (case insensitive) value recognized",
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"m=|metadata=","The metadata output format: 0 for JSON, 1 for TXT, 2 for None (no output); both numeric and text (case insensitive) value recognized. Defaults to None",
For running on Windows, omit `mono`. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata `-m=0|1` (0 for JSON, 1 for TXT) and the spectra file `-f=0|1|2|3` (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet) or both. Use the `-p` flag to disable the thermo native peak picking.
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For running on Windows, omit `mono`. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata `-m=0|1` (0 for JSON, 1 for TXT) and the spectra file `-f=0|1|2|3|4` (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for no output) or both. Use the `-p` flag to disable the thermo native peak picking.
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```
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ThermoRawFileParser.exe --help
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Usage is ThermoRawFileParser.exe [subcommand] [options]
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optional subcommands are xic|query (use [subcommand] -h for more info]):
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-h, --help Prints out the options.
@@ -60,23 +59,25 @@ optional subcommands are xic|query (use [subcommand] -h for more info]):
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-d, --input_directory=VALUE
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The directory containing the raw files (Required).
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Specify this or an input raw file -i.
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-o, --output=VALUE The output directory. Specify this or an output
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file -b. Specifying neither writes to the input
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directory.
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-b, --output_file=VALUE The output file. Specify this or an output
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-b, --output=VALUE The output file. Specify this or an output
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directory -o. Specifying neither writes to the
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input directory.
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-o, --output_directory=VALUE
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The output directory. Specify this or an output
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file -b. Specifying neither writes to the input
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directory.
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-s, --stdout Write to standard output. Cannot be combined with
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file or directory output. Implies silent logging,
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i.e. logging level 0
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-f, --format=VALUE The spectra output format: 0 for MGF, 1 for mzML,
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2 for indexed mzML, 3 for Parquet; both numeric
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and text (case insensitive) value recognized.
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Defaults to indexed mzML if no format is
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specified.
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-m, --metadata=VALUE The metadata output format: 0 for JSON, 1 for TXT;
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both numeric and text (case insensitive) value
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recognized
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2 for indexed mzML, 3 for Parquet, 4 for None (
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no output); both numeric and text (case
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insensitive) value recognized. Defaults to
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indexed mzML if no format is specified.
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-m, --metadata=VALUE The metadata output format: 0 for JSON, 1 for TXT,
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2 for None (no output); both numeric and text (
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case insensitive) value recognized. Defaults to
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None
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-c, --metadata_output_file=VALUE
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The metadata output file. By default the metadata
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file is written to the output directory.
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S3 bucket name
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```
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Output file extension is determined by the used output format and (optional) gzip compression, for example, if format is MGF without gzip compression, the output file will receive `.mgf` extension, if format is mzML with gzip compression the output file will have `.mzML.gz` extension. All user input will be standardized to fulfill abovementioned requrements.
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Output file extension is determined by the used output format and (optional) gzip compression, for example, if format is MGF without gzip compression, the output file will receive `.mgf` extension, if format is mzML with gzip compression the output file will have `.mzML.gz` extension. All user input will be standardized to fulfill abovementioned requirements.
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A (java) graphical user interface is also available [here](https://github.com/compomics/ThermoRawFileParserGUI) that enables the selection of an input RAW directory or one ore more RAW files.
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@@ -137,7 +138,7 @@ usage is:
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-h, --help Prints out the options.
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-i, --input=VALUE The raw file input (Required).
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-n, --scans=VALUE The scan numbers. e.g. "1-5, 20, 25-30"
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-b, --output_file=VALUE The output file. Specifying none writes the output
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-b, --output=VALUE The output file. Specifying none writes the output
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file to the input file parent directory.
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-p, --noPeakPicking Don't use the peak picking provided by the native
-p, --print_example Show a json input file example.
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-o, --output=VALUE The output directory. Specify this or an output
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file. Specifying neither writes to the input
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directory.
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-b, --output_file=VALUE The output file. Specify this or an output
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-b, --output=VALUE The output file. Specify this or an output
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directory. Specifying neither writes to the
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input directory.
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-o, --output_directory=VALUE
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The output directory. Specify this or an output
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file. Specifying neither writes to the input
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directory.
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-6, --base64 Encodes the content of the xic vectors as base 64
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encoded string.
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-s, --stdout Pipes the output into standard output. Logging is
@@ -192,7 +194,8 @@ Provide one of the following filters:
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* M/Z start and end
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* sequence and tolerance (tolerance unit optional, defaults to `ppm`)
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optionally one can define starting and ending retention times and thermo filter string (defaults to `ms`)
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optionally one can define starting and ending retention times, provide filter string (defaults to `ms`, i.e. only MS1 scans), and a comment (free text) field; any valid filter string is supported,
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however only basic validation is performed, see [issue #158](https://github.com/compomics/ThermoRawFileParser/issues/158) for details. Comment can contain any text and will be preserved in the output.
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