Input file or directory containing the data to convert. This may be:#br#- a single file in a multi-purpose XML format (.pepXML, .protXML, .idXML, .mzid),#br#- a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),#br#- a single file in fasta format (can only be used to generate a theoretical mzML),#br#- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),#br#- for Sequest results, a directory containing .out files.#br# [pepXML,protXML,mascotXML,omssaXML,xml,psms,tsv,idXML,mzid,xquest.xml,fasta]

[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file [mzML,mzXML,mzData,opt.]