Suggestion: how about a Stringlist with actual names instead of numbers? 
Could be translated internally if msgf takes ints...

On 7. Mai 2014 13:59:45 MESZ, Stephan Aiche <notifications@github.com> wrote:
>> +    setValidFormats_("database",
>ListUtils::create<String>("FASTA"));
>> +
>> +    registerInputFile_("msgfplus_executable", "<executable>", "",
>"MSGFPlus executable of the installation e.g. 'java - jar
>MSGFPlus.jar'");
>> +
>> +    registerDoubleOption_("precursor_mass_tolerance", "<tolerance>",
>20, "Precursor mono mass tolerance.", false);
>> +    registerStringOption_("precursor_mass_tolerance_unit", "<unit>",
>"ppm", "Unit to be used for precursor mass tolerance.", false);
>> +    setValidStrings_("precursor_mass_tolerance_unit",
>ListUtils::create<String>("Da,ppm"));
>> +
>> +    registerStringOption_("isotope_error_range", "<range>", "0,1",
>"Range of allowed isotope peak errors. Takes into account of the error
>introduced by chooosing a non-monoisotopic peak for fragmentation. The
>combination of -t and -ti determins the precursor mass tolerance. E.g.
>-precursor_mass_tolerance 20 -precursor_mass_tolerance_unit ppm
>-isotope_error_range -1,2 tests abs(exp-calc-n*1.00335Da)<20ppm for
>n=-1, 0, 1, 2", false);
>> +
>> +    registerIntOption_("decoy", "<0/1>", 0, "0: don't search decoy
>database, 1: search decoy database", false);
>> +    registerIntOption_("fragment_method", "<method>", 0, "0: As
>written in the spectrum or CID if no info, 1: CID, 2: ETD, 3: HCD",
>false);
>> +    registerIntOption_("instrument", "<instrument>", 0, "0: Low-res
>LCQ/LTQ, 1: High-res LTQ, 2: TOF, 3: Q-Exactive", false);
>> +    registerIntOption_("enzyme", "<enzyme>", 1, "0: unspecific
>cleavage, 1: Trypsin, 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: glutamyl
>endopeptidase, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: no cleavage", false);
>> +    registerIntOption_("protocol", "<protocol>", 0, "0: NoProtocol,
>1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT", false);    
>> +    registerIntOption_("tolerable_termini", "<num>", 2, "For
>trypsin, 0: non-tryptic, 1: semi-tryptic, 2: fully-tryptic peptides
>only.", false);
>
>maybe you could set min/max values for the above options, as it will
>guarantee that you only pass valid values to msgf+
>
>---
>Reply to this email directly or view it on GitHub:
>https://github.com/OpenMS/OpenMS/pull/803/files#r12372417

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