public WorkflowParameters(ArgumentParser.ParseOptions parseOptions)
{
ParseParams = new ParseWorkflowParameters();
ExpType = ExperimentType.DDA;
MgfIntensityCutoff = parseOptions.IntensityCutoff;
MgfMassCutoff = parseOptions.MassCutOff;
InputFiles = parseOptions.InputFiles;
RawFileDirectory = parseOptions.InputDirectory;
RefineMassCharge = parseOptions.RefineMassCharge;
ParseParams.Chromatogram = parseOptions.Chromatogram;
ParseParams.LabelingReagents = String.Empty;
ParseParams.LabelingReagents = parseOptions.LabelingReagents;
ParseParams.Metrics = parseOptions.Metrics;
ParseParams.Parse = parseOptions.ParseData;
ParseParams.Quant = parseOptions.Quant;
ParseParams.UnlabeledQuant = parseOptions.UnlabeledQuant;
ParseParams.WriteMgf = parseOptions.WriteMGF;
if (parseOptions.OutputDirectory != null)
{
if (!Path.IsPathRooted(parseOptions.OutputDirectory))
{
parseOptions.OutputDirectory = Path.Combine(Directory.GetCurrentDirectory(), parseOptions.OutputDirectory);
}
}
ParseParams.OutputDirectory = parseOptions.OutputDirectory;
}
public WorkflowParameters()
{
QcParams = new QcWorkflowParameters();
ParseParams = new ParseWorkflowParameters();
}