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Intermediate results
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| # DO NOT EDIT | ||
| # DeCoSTAR: computing ancestral adjacencies | ||
| ecceTERA_DeCoSTAR: | ||
| name: &decostar_name 'ecceTERA_DeCoSTAR' | ||
| input: | ||
| dirs: | ||
| - &decostar_input_dir !join [*dir_aux, *decostar_name] | ||
| files: | ||
| - &decostar_input_file_trees !join [*decostar_input_dir, 'gene_trees.txt'] | ||
| - &decostar_input_file_adjacencies !join [*decostar_input_dir, 'adjacencies.txt'] | ||
| script: | ||
| - !join [*run_dir_scripts, 'DeCoSTAR_create_input_files.py'] | ||
| - !ref [*data_gene_orders_path] | ||
| - !ref [*decostar_input_path] | ||
| - !ref [*data_families_path] | ||
| - !ref [*decostar_input_file_adjacencies] | ||
| - !ref [*decostar_input_file_trees] | ||
| output: | ||
| file: &decostar_output_file !ref [*data_adjacencies_path] | ||
| slurm: | ||
| options: !ref [*decostar_slurm_options] | ||
| modules: !ref [*decostar_modules] | ||
| array: | ||
| results: | ||
| file: &decostar_slurm_array_results_file !ref [*data_species_path] | ||
| field: &decostar_slurm_array_results_field 1 | ||
| var: &decostar_slurm_array_results_var 'SPECIES' | ||
| name: &decostar_slurm_array_results_name !concat ['${', *decostar_slurm_array_results_var, '}'] | ||
| ext: &decostar_slurm_array_results_ext !ref [*data_adjacencies_ext] | ||
| results: | ||
| dirs: | ||
| - &decostar_results_dir !join [*dir_results, *decostar_name] | ||
| names: | ||
| - &decostar_slurm_results_species_adjacencies_name !concat [*decostar_slurm_array_results_name, *decostar_slurm_array_results_ext] | ||
| files: | ||
| - &decostar_slurm_results_species_adjacencies !join [*decostar_results_dir, *decostar_slurm_results_species_adjacencies_name] | ||
| other: | ||
| - &decostar_slurm_results_adjacencies_file !join [*decostar_results_dir, 'adjacencies.txt'] | ||
| - &decostar_slurm_results_genes_file_1 !join [*decostar_results_dir, 'genes.txt'] | ||
| - &decostar_slurm_results_genes_file_2 !join [*decostar_results_dir, 'genes_reformatted.txt'] | ||
| - &decostar_slurm_results_species_file !join [*decostar_results_dir, 'species.txt'] | ||
| - &decostar_slurm_results_species_tree_file !join [*decostar_results_dir, 'speciesTree.phyloxml'] | ||
| - &decostar_slurm_results_reconciliations_file !join [*decostar_results_dir, 'reconciliations.xml'] | ||
| cmd: | ||
| - !concat [*decostar_exec, ' \'] | ||
| # Input files | ||
| - !concat [' species.file=', *data_species_tree_path, ' \'] | ||
| - !concat [' adjacencies.file=', *decostar_input_file_adjacencies, ' \'] | ||
| - !concat [' gene.distribution.file=', *decostar_input_file_trees, ' \'] | ||
| # Output | ||
| - !concat [' output.dir=', *decostar_results_dir, ' \'] | ||
| - !concat [' write.newick=', *decostar_write_newick, ' \'] | ||
| - !concat [' write.adjacency.trees=', *decostar_write_adjacency_trees, ' \'] | ||
| # Model | ||
| - !concat [' already.reconciled=', *decostar_already_reconciled, ' \'] | ||
| - !concat [' rooted=', *decostar_rooted, ' \'] | ||
| - !concat [' nb.sample=', *decostar_nb_sample, ' \'] | ||
| - !concat [' dupli.cost=', *decostar_dupli_cost, ' \'] | ||
| - !concat [' loss.cost=', *decostar_loss_cost, ' \'] | ||
| - !concat [' AGain.cost=', *decostar_again_cost, ' \'] | ||
| - !concat [' ABreak.cost=', *decostar_abreak_cost, ' \'] | ||
| - !concat [' Loss.aware=', *decostar_loss_aware, ' \'] | ||
| - !concat [' Loss.iteration=', *decostar_loss_iteration, ' \'] | ||
| - !concat [' C1.Advantage=', *decostar_c1_advantage, ' \'] | ||
| - !concat [' all.pair.equivalence.class=', *decostar_all_pairs, ' \'] | ||
| - !concat [' always.AGain=', *decostar_always_again, ' \'] | ||
| - !concat [' absence.penalty=', *decostar_absence_penalty, ' \'] | ||
| - !concat [' all.pair.equivalence.class=', *decostar_all_pairs, ' \'] | ||
| - !concat [' boltzmann.temperature=', *decostar_boltzmann_temperature, ' \'] | ||
| - ' write.adjacencies=true \' | ||
| - ' write.genes=true \' | ||
| - ' use.boltzmann=true \' | ||
| - ' char.sep="|" \' | ||
| - ' with.transfer=false \' | ||
| - ' verbose=2' | ||
| - ' ' | ||
| - !concat [!join [*run_dir_scripts, 'DeCoSTAR_reformat.py'], ' \'] | ||
| - !concat [' ', *data_species_path, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_species_file, ' \'] | ||
| - !concat [' ', *decostar_already_reconciled, ' \'] | ||
| - !concat [' ', *data_families_path, ' \'] | ||
| - !concat [' ', *decostar_input_path, ' \'] | ||
| - !concat [' ', *decostar_input_file_trees, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_genes_file_1, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_adjacencies_file, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_genes_file_2, ' \'] | ||
| - !concat [' ', *decostar_results_dir] | ||
| - ' ' | ||
| - !concat [!join [*run_dir_scripts, 'DeCoSTAR_ecceTERA_reformat.py'], ' \'] | ||
| - !concat [' ', *decostar_slurm_results_genes_file_1, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_genes_file_2, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_species_tree_file, ' \'] | ||
| - !concat [' ', *decostar_slurm_results_reconciliations_file, ' \'] | ||
| - !concat [' ', *decostar_results_dir, ' \'] | ||
| - !concat [' ', *data_reconciliations_ext, ' \'] | ||
| - !concat [' ', *data_reconciliations_path] | ||
| stats: | ||
| names: | ||
| - &decostar_stats_file_adj_species_name !concat [*decostar_name, '_adjacencies_species', *log_ext_stat] | ||
| - &decostar_stats_file_adj_components_name !concat [*decostar_name, '_adjacencies_components', *log_ext_stat] | ||
| - &decostar_stats_file_rec_species_name !concat [*decostar_name, '_reconciliations_species', *log_ext_stat] | ||
| - &decostar_stats_file_rec_families_name !concat [*decostar_name, '_reconciliations_families', *log_ext_stat] | ||
| files: | ||
| - &decostar_stats_file_adj_species !join [*dir_stats, *decostar_name, *decostar_stats_file_adj_species_name] | ||
| - &decostar_stats_file_adj_components !join [*dir_stats, *decostar_name, *decostar_stats_file_adj_components_name] | ||
| - &decostar_stats_file_rec_species !join [*dir_stats, *decostar_name, *decostar_stats_file_rec_species_name] | ||
| - &decostar_stats_file_rec_families !join [*dir_stats, *decostar_name, *decostar_stats_file_rec_families_name] | ||
| script: | ||
| - !join [*run_dir_scripts, 'recPhyloXML_statistics.py'] | ||
| - !ref [*data_reconciliations_path] | ||
| - !ref [*decostar_stats_file_rec_species] | ||
| - !ref [*decostar_stats_file_rec_families] | ||
| - !concat [';'] | ||
| - !join [*run_dir_scripts, 'DeCoSTAR_statistics.py'] | ||
| - !ref [*data_species_path] | ||
| - !ref [*decostar_slurm_results_genes_file_2] | ||
| - !ref [*data_adjacencies_path] | ||
| - !ref [*decostar_stats_thresholds] | ||
| - !ref [*decostar_stats_file_adj_species] | ||
| - !concat [';'] | ||
| - !join [*run_dir_scripts, 'gene_orders_utils.py'] | ||
| - 'stats' | ||
| - !ref [*decostar_slurm_results_genes_file_2] | ||
| - !ref [*data_adjacencies_path] | ||
| - !ref [*decostar_results_dir] | ||
| - !ref [*decostar_stats_file_adj_components] |
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