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Taking out 'both' option of contamination loop

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Auden Cote-L'Heureux 2025-03-28 15:40:58 -04:00 committed by GitHub
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commit d161957d86
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PTL2/Scripts/utils.py
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@ -47,7 +47,7 @@ def get_params():
core.add_argument('--allow_large_files', action = 'store_true', help = 'Allow files with more than 2,000 sequences to run through Guidance.')
CL = parser.add_argument_group('Contamination loop parameters')
CL.add_argument('--contamination_loop', default = None, choices = {'seq', 'clade', 'both'}, help = 'Remove sequences by looking at the sisters of each sequence in a rules file or by picking the best clades')
CL.add_argument('--contamination_loop', default = None, choices = {'seq', 'clade'}, help = 'Remove sequences by looking at the sisters of each sequence in a rules file or by picking the best clades')
CL.add_argument('--nloops', default = 10, type = int, help = 'The maximum number of contamination-removal loops')
CL.add_argument('--cl_tree_method', default = 'fasttree', choices = {'iqtree', 'raxml', 'fasttree', 'iqtree_fast'}, help = 'Tree-building method to use in each contamination loop iteration.')
CL.add_argument('--cl_alignment_method', default = 'mafft_only', choices = {'mafft_only', 'guidance'}, help = 'Alignment method to use in each contamination loop iteration.')