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Changing default output location in utils.py

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Auden Cote-L'Heureux 2024-05-29 12:44:15 -04:00 committed by GitHub
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commit 426d51ea85
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PTL2/Scripts/utils.py
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@ -26,7 +26,7 @@ def get_params():
common.add_argument('--gf_list', default = None, help = 'Path to the file with the GFs of interest. Only required if starting from the raw dataset.')
common.add_argument('--taxon_list', default = None, help = 'Path to the file with the taxa (10-digit codes) to include in the output.')
common.add_argument('--data', help = 'Path to the input dataset. The format of this varies depending on your --start parameter. If you are running the contamination loop starting with trees, this folder must include both trees AND a fasta file for each tree (with identical file names other than the extension) that includes an amino-acid sequence for each tip of the tree (with the sequence names matching exactly the tip names).')
common.add_argument('--output', default = '../', help = 'Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts.')
common.add_argument('--output', default = './', help = 'Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts.')
common.add_argument('--force', action = 'store_true', help = 'Overwrite all existing files in the "Output" folder.')
common.add_argument('--tree_method', default = 'iqtree', choices = {'iqtree', 'raxml', 'all'}, help = 'Program to use for tree-building')
common.add_argument('--blacklist', type = str, help = 'A text file with a list of sequence names not to consider')