<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="MOMO @SERVICE_VERSION@">
    <usage>MOMO: post-translational modification motifs</usage>
    <info>
    <![CDATA[
momo [options] [-ptm <ptm file>
                            [ -filter_field <encoded field name> 
                              -filter_type lt|lteq|eq|gteq|gt 
                              -filter_thresh <threshold> ]? ]+

  PSM arguments:
    -ptm <ptm file>                       Specify a PTM file for processing
    -ptm-type <type>                      comet|ms-gf+|tide|percolator
    -psm-column-name <name>               Name of column containing modified peptides
                                          (PTM file(s) must be in PSM format)
    -filter_field <encoded field name>    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 <threshold>            Specify the number used to filter the
                                           previously specified PSM file.
    -db-background                        use the flank file for background peptides
    -flank <FASTA file>                   Specify a protein FASTA file
                                           containing flanking sequence;
                                           any paths begining with db/ are
                                           pre-existing databases.
    -occurs <num>                         Set the minimum number of occurences.
    -width <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.
    ]]>
    </info>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/momo_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
