void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Input file annotated by ProteinQuantifier");
setValidFormats_("in", ListUtils::create<String>("idXML"));
registerOutputFile_("out", "<file>", "", "Output file (mzTab)", true);
setValidFormats_("out", ListUtils::create<String>("csv"));
}
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "",
"Input file (see below for details)");
setValidFormats_("in", ListUtils::create<String>("mzML,idXML,featureXML,consensusXML"));
registerOutputFileList_("out", "<file(s)>", StringList(), "Output file(s)");
setValidFormats_("out", ListUtils::create<String>("featureXML"));
addEmptyLine_();
registerFlag_("use_peptide_mass", "[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)");
}