MOMO: post-translational modification motifs [ -filter_field -filter_type lt|lteq|eq|gteq|gt -filter_thresh ]? ]+ PSM arguments: -ptm Specify a PTM file for processing -ptm-type comet|ms-gf+|tide|percolator -psm-column-name Name of column containing modified peptides (PTM file(s) must be in PSM format) -filter_field Specify a field of the previously specified PSM file to filter on. -filter_type lt|lteq|eq|gteq|gt Specify the filtering type for the previously specified PSM file as: lt - less than, le - less than or equal, eq - equal, ge - greater than or equal, or gt - greater than. -filter_thresh Specify the number used to filter the previously specified PSM file. -db-background use the flank file for background peptides -flank Specify a protein FASTA file containing flanking sequence; any paths begining with db/ are pre-existing databases. -occurs Set the minimum number of occurences. -width Set the width of the motifs. -remove-unknowns modified peptides will be removed if they contain 'X' -single-per-mass A single motif will be generated for each distinct modification mass. -harvard emulate original motif-x (including p-value hack) -help Show this brief help message. ]]> @SERVICE_DIR@/momo_webservice @drmaa_queue@ false