It's not in the online command-line manual, but it's in the usage
statement for omssacl:
G:\work\omssa\omssa-2.1.7.win32>omssacl
USAGE
omssacl.exe [-h] [-help] [-xmlhelp] [-pm param] [-d blastdb] [-umm]
[-f infile] [-fx xmlinfile] [-fb dtainfile] [-fp pklinfile]
[-fm pklinfile] [-foms omsinfile] [-fomx omxinfile] [-fbz2 bz2infile]
[-fxml omxinfile] [-o textasnoutfile] [-ob binaryasnoutfile]
[-ox xmloutfile] [-obz2 bz2outfile] [-op pepxmloutfile] [-oc
csvfile] [-w]
[-to pretol] [-te protol] [-tom promass] [-tem premass] [-tez prozdep]
[-ta autotol] [-tex exact] [-i ions] [-cl cutlo] [-ch cuthi] [-ci
cutinc]
[-cp precursorcull] [-v cleave] [-x taxid] [-w1 window1] [-w2 window2]
[-h1 hit1] [-h2 hit2] [-hl hitlist] [-ht tophitnum] [-hm minhit]
[-hs minspectra] [-he evalcut] [-mf fixedmod] [-mv variablemod] [-mnm]
[-mm maxmod] [-e enzyme] [-zh maxcharge] [-zl mincharge]
[-zoh maxprodcharge] [-zt chargethresh] [-z1 plusone] [-zc calcplusone]
[-zcc calccharge] [-pc pseudocount] [-sb1 searchb1] [-sct searchcterm]
[-sp productnum] [-scorr corrscore] [-scorp corrprob] [-no minno]
[-nox maxno] [-is subsetthresh] [-ir replacethresh] [-ii
iterativethresh]
[-p prolineruleions] [-il] [-el] [-ml] [-mx modinputfile]
[-mux usermodinputfile] [-nt numthreads] [-ni] [-ns] [-os] [-nrs]
[-logfile File_Name] [-conffile File_Name] [-version] [-version-full]
[-dryrun]
-op is the option you're looking for.
-Matt
Loďc JOFFRE wrote:
> Hello David,
>
> I was looking everywhere on my OMSSA browser and in the OMSSA on line
> and I really do not see any option to output pepxml or any pepxml
> converter...
> Are you considering that .omx files are pepxml files?
> Because I could not use its on TPP...
> Could you give me the steps to output pepxml on OMSSA?
>
> Thanks in advance,
> best regards,
>
> Loďc
>
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