--- a/fimo_wrapper.py	Fri Jun 17 13:15:48 2016 -0400
+++ b/fimo_wrapper.py	Wed Jun 29 08:35:04 2016 -0400
@@ -56,13 +56,13 @@
 parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score')
 parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store')
 parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id')
-parser.add_argument('--output_separate_motifs', default="no", help='Output one dataset per motif')
+parser.add_argument('--output_separate_motifs', dest='output_separate_motifs', default='no', help='Output one dataset per motif')
 parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix')
 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value')
 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand')
 parser.add_argument('--output_path', dest='output_path', help='Output files directory')
-parser.add_argument('--parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
-parser.add_argument('--remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
+parser.add_argument('--parse_genomic_coord', dest='parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
+parser.add_argument('--remove_duplicate_coords', dest='remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold')
 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold')
 parser.add_argument('--gff_output', dest='gff_output', help='Gff output file')