| Previous changeset 5:eca84de658b0 (2016-06-17) Next changeset 7:b3f7ff168b9a (2016-07-07) |
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modified:
fimo.xml fimo_wrapper.py |
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| diff -r eca84de658b0 -r cdcc4bb60bc3 fimo.xml --- a/fimo.xml Fri Jun 17 13:15:48 2016 -0400 +++ b/fimo.xml Wed Jun 29 08:35:04 2016 -0400 |
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| @@ -117,7 +117,10 @@ <option value="yes">Yes</option> </param> <when value="yes"> - <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" /> + <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> </when> <when value="no"/> </conditional> |
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| diff -r eca84de658b0 -r cdcc4bb60bc3 fimo_wrapper.py --- a/fimo_wrapper.py Fri Jun 17 13:15:48 2016 -0400 +++ b/fimo_wrapper.py Wed Jun 29 08:35:04 2016 -0400 |
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| @@ -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') |