def setUp(self): com1 = Command( 'Summarize Taxa', 'summarize_taxa_through_plots.py', '{"--otu_table_fp":null}', '{}', '{"--mapping_category":null, "--mapping_fp":null,' '"--sort":null}', '{"--output_dir":null}') com2 = Command( 'Beta Diversity', 'beta_diversity_through_plots.py', '{"--otu_table_fp":null,"--mapping_fp":null}', '{}', '{"--tree_fp":null,"--color_by_all_fields":null,' '"--seqs_per_sample":null}', '{"--output_dir":null}') com3 = Command( 'Alpha Rarefaction', 'alpha_rarefaction.py', '{"--otu_table_fp":null,"--mapping_fp":null}', '{}', '{"--tree_fp":null,"--num_steps":null,' '"--min_rare_depth"' ':null,"--max_rare_depth":null,' '"--retain_intermediate_files":false}', '{"--output_dir":null}') self.all_comms = { "16S": [com1, com2, com3], "18S": [com1, com2, com3], "ITS": [com2, com3], "Proteomic": [com2, com3], "Metabolomic": [com2, com3], "Metagenomic": [com2, com3], }
def test_get_commands(self): exp = [ Command('Summarize Taxa', 'summarize_taxa_through_plots.py', '{"--otu_table_fp":null}', '{}', '{"--mapping_category":null, "--mapping_fp":null,' '"--sort":null}', '{"--output_dir":null}'), Command('Beta Diversity', 'beta_diversity_through_plots.py', '{"--otu_table_fp":null,"--mapping_fp":null}', '{}', '{"--tree_fp":null,"--color_by_all_fields":null,' '"--seqs_per_sample":null}', '{"--output_dir":null}'), Command('Alpha Rarefaction', 'alpha_rarefaction.py', '{"--otu_table_fp":null,"--mapping_fp":null}', '{}', '{"--tree_fp":null,"--num_steps":null,''"--min_rare_depth"' ':null,"--max_rare_depth":null,' '"--retain_intermediate_files":false}', '{"--output_dir":null}') ] self.assertEqual(Job.get_commands(), exp)