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Fixing concat taxon list read error

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Katzlab 2024-08-22 11:59:58 -04:00 committed by GitHub
parent 41cc1354b3
commit 7904ec8b35
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PTL2/Scripts/utils.py
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@ -65,7 +65,7 @@ def get_params():
other = parser.add_argument_group('Other arguments')
other.add_argument('--concatenate', action = 'store_true', help = 'Remove paralogs and generate an alignment for concatenation')
other.add_argument('--concat_target_taxa', nargs = '+', default = None, help = 'The taxonomic group (sequence prefix), groups, or a file containing a list of groups (multiple prefixes) for which to select sequences to construct a concatenated alignment')
other.add_argument('--concat_target_taxa', type = str, default = None, help = 'The taxonomic group (sequence prefix), groups, or a file containing a list of groups (multiple prefixes) for which to select sequences to construct a concatenated alignment')
other.add_argument('--tree_font_size', default = 12, help = "Change this if you're not quite happy with the font size in the output trees. If you want smaller font in your trees, you can lower this value; and if you want larger font in your trees, you can raise this value. Some common values are 8, 10, and 12. Size 16 font is pretty big, and size 4 font is probably too small for most purposes. Iconoclasts use size 9, 11, or 13 font.")
other.add_argument('--keep_temp', action = 'store_true', help = "Use this to keep ALL Guidance intermediate files")
other.add_argument('--keep_iter', '-z', action = 'store_true', help = 'Keep all Guidance iterations (beware this will be very large)')