Mercurial > repos > geert-vandeweyer > cuffcompare
changeset 1:15437246f588 draft
corrected boolean argument handling in wrapper.py
| author | geert-vandeweyer |
|---|---|
| date | Fri, 01 Aug 2014 11:01:51 -0400 |
| parents | d4455014134b |
| children | 5ac3ca7ad18b |
| files | cuffcompare_wrapper.py |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/cuffcompare_wrapper.py Fri Aug 01 10:49:19 2014 -0400 +++ b/cuffcompare_wrapper.py Fri Aug 01 11:01:51 2014 -0400 @@ -17,11 +17,11 @@ parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') - parser.add_option( '-M', dest='discard_single_exon_all', help='discard (ignore) single-exon transfrags and reference transcript') - parser.add_option( '-N', dest='discard_single_exon_ref', help='discard (ignore) single-exon reference transcripts') + parser.add_option( '-M', action="store_true", dest='discard_single_exon_all', help='discard (ignore) single-exon transfrags and reference transcript') + parser.add_option( '-N', action="store_true", dest='discard_single_exon_ref', help='discard (ignore) single-exon reference transcripts') parser.add_option( '-e', dest='max_dist_exon', help='Max. Distance for assessing exon accuracy" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100') parser.add_option( '-d', dest='max_dist_group', help='Max.Distance for transcript grouping" help="max. distance (range) for grouping transcript start sites. Default: 100') - parser.add_option( '-F', dest='discard_redundant_intron_transfrags', help='Discard intron-redundant transfrags if they share the 5-prime end (if they differ only at the 3-prime end)') + parser.add_option( '-F', action="store_true", dest='discard_redundant_intron_transfrags', help='Discard intron-redundant transfrags if they share the 5-prime end (if they differ only at the 3-prime end)') # Wrapper / Galaxy options. parser.add_option( '', '--index', dest='index', help='The path of the reference genome' )