raxml: add python requirement #2707
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ad fix test data
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bump? |
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Yes, please. |
| OM: CLI options DEBUG START: | ||
| <Values at 0x7f8e104919e0: {'bootseed': None, 'groupingfile': None, 'posterior_bootstopping_analysis': None, 'print_branch_lengths': None, 'starting_tree': None, 'model_opt_precision': None, 'weightfile': None, 'use_median_approximation': None, 'majority_rule_consensus': None, 'excludefile': None, 'save_memory_gappy_alignments': None, 'binary': 'raxmlHPC', 'numofcats': None, 'multistate_sub_model': None, 'multiple_model': None, 'search_complete_random_tree': None, 'source': '/tmp/tmpS1corm/files/000/dataset_7.dat', 'outgroup_name': None, 'estimate_individual_branch_lengths': None, 'ml_search_convergence': None, 'file_multiple_trees': None, 'rapid_bootstrap_random_seed': None, 'random_seed': 1234567890, 'disable_undetermined_seq_check': None, 'save_memory_cat_model': None, 'enable_evol_heuristics': None, 'aa_empirical_freq': None, 'threads': 1, 'external_protein_model': None, 'search_algorithm': 'd', 'constraint_file': None, 'secondary_structure_model': None, 'number_of_runs': 5, 'name': None, 'initial_rearrangement_setting': None, 'secondary_structure_file': None, 'model_type': 'nucleotide', 'aa_search_matrix': None, 'disable_rate_heterogeneity': None, 'base_model': 'GTRCAT', 'parsimony_starting_tree_only': None, 'number_of_runs_bootstop': None, 'sliding_window_size': None, 'bin_model_parameter_file': None}> | ||
| OM: CLI options DEBUG END | ||
| RAxML_parsimonyTree.galaxy.RUN.0 |
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Is it expected that the test data output changed so much ? Could these changes be due to galaxyproject/galaxy#9052 as well ?
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this output is a (extended) newick format. It seems that originally the content of the log file was used for this output.
I just added the ftype="nhx" attribute to the test outputs .. but I guess this won't help anyway since nhx has no sniffer (yet).
Also in my opinion the output is wrong since the names between the trees are not allowed. Question is is downstream tools silently accept this or if we should change it (it comes from the Galaxy tool specific py script)
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I'd be in favor of adhering to the correct format. 5f148a7 does this, correct ?
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To the best of my knowledge, yes.
and fix test data
FOR CONTRIBUTOR: