diff --git a/RawTools/ArgumentParser.cs b/RawTools/ArgumentParser.cs index ee4dd6a..9dd2588 100644 --- a/RawTools/ArgumentParser.cs +++ b/RawTools/ArgumentParser.cs @@ -49,7 +49,7 @@ class ParseOptions public string InputDirectory { get; set; } [Option('p', "parse", HelpText = "Optional. Parses raw file meta and scan data and writes the output to a tab-delimited text file. " + - "Either this output or the quant output (-q) is recommended unless your aim is to simply create an MGF or to observe broad metrics using -x.")] + "Typically either this output or the quant output (-q) is used unless your aim is to simply create an MGF or to observe broad metrics using -x.")] public bool ParseData { get; set; } [Option('q', "quant", HelpText = "Optional. Similar to parse (-p), but also quantifies reporter ions and write results to output matrix. " + @@ -98,14 +98,14 @@ class QcOptions [Option('d', "directory", Required = true, HelpText = "Path to the directory containing the raw files for QC")] public string DirectoryToQc { get; set; } - [Option('q', "qcdirectory", Required = true, HelpText = "Path to the directory containing (or to contain) the QC data file (called QC.qc)")] + [Option('q', "qcdirectory", Required = true, HelpText = "Path to the directory containing (or to contain) the QC data file (called QC.xml)")] public string QcDirectory { get; set; } - [Option('s', "search", Required = false, HelpText = "Specify a search algorith to facilitate the calculation of identification related metrics. " + + [Option('s', "search", Required = false, HelpText = "Specify the search engine to facilitate the calculation of identification related metrics. " + "Must be one of the following: {identipy, xtandem}")] public string SearchAlgorithm { get; set; } - [Option('i', "identipy", HelpText = "DEPRECATED. This argument will be replaced with the more general -s (--search) in a future version." + + [Option('i', "identipy", HelpText = "[DEPRECATED. This argument will be replaced with the more general -s (--search) in a future version.]" + "Optional. Perform an IdentiPy search on a subset of " + "the ms2 scans in the raw file to get identification-related metrics as part of the QC.")] public bool Identipy { get; set; } @@ -140,10 +140,10 @@ class QcOptions "Include the extension if there is one. -I and -p must be invoked together.")] public string IdentipyScript { get; set; } - [Option('X', "xtandemdirectory", HelpText = "Specify the path to the X! Tandem directory.")] + [Option('X', "xtandemdirectory", HelpText = "Specify the path to the X! Tandem directory (the directory containing \"tandem.exe\").")] public string XTandemDirectory { get; set; } - [Option('N', "numberspectra", Default = 10000, HelpText = "Optional. The number of MS2 spectra used for the Identipy search. Defaults to 10,000. " + + [Option('N', "numberspectra", Default = 10000, HelpText = "Optional. The number of MS2 spectra to be passes to the search engine as an MGF file. Defaults to 10,000. " + "If N is greater than the number of MS2 scans in a raw file, all MS2 scans will be used.")] public int NumberSpectra { get; set; } @@ -157,7 +157,7 @@ class QcOptions public double IntensityCutoff { get; set; } [Option("fixedscans", HelpText = "Causes the scans in the mgf file used for a database search to be static (i.e. not random, the same " + - "scans are used everytime). This is intended for diagnostic purposes, not for general use.")] + "scans are used everytime). This is intended for testing purposes, not for general use.")] public bool FixedScans { get; set; } } } diff --git a/changelog.md b/changelog.md index a2fd4ac..3a76f60 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Added - Added support for X! Tandem as a search engine. +- Chromatograms of raw files can be exported as tab-delimited text files using `--chro` as an argument. See `RawTools.exe parse --help` for more info. ### Deprecated - The `-i` argument for invoking an IdentiPy search has been deprecated and will not be available in future releases. Instead, please use `-s identipy` to