Mercurial > repos > galaxyp > map_peptides_to_bed
diff map_peptides_to_bed.py @ 4:88d2c4c2cb0a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
| author | galaxyp |
|---|---|
| date | Mon, 22 Feb 2016 17:31:34 -0500 |
| parents | c770d523bd28 |
| children | aac354f8d5e8 |
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--- a/map_peptides_to_bed.py Tue Jan 12 21:02:24 2016 -0500 +++ b/map_peptides_to_bed.py Mon Feb 22 17:31:34 2016 -0500 @@ -232,7 +232,7 @@ parser.add_option( '-t', '--translated_bed', dest='translated_bed', default=None, help='A bed file with added 13th column having a translation' ) parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' ) parser.add_option( '-p', '--peptide_column', type='int', dest='peptide_column', default=1, help='column ordinal with peptide sequence' ) - parser.add_option( '-n', '--name_column', type='int', dest='name_column', default=None, help='column ordinal with protein name' ) + parser.add_option( '-n', '--name_column', type='int', dest='name_column', default=2, help='column ordinal with protein name' ) parser.add_option( '-s', '--start_column', type='int', dest='start_column', default=None, help='column with peptide start position in protein' ) parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation' ) ## parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file' )