view test-data/summarize/bracken_full_output.json @ 0:6e868bf6c38e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
author iuc
date Tue, 30 Apr 2024 08:42:33 +0000
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[{"analysis_software_version": "2.8", "reference_database_version": "PlusPF_16", "analysis_software_name": "bracken", "results": [{"name": "bracken_report", "file_path": "tests/data/dummy/bracken/bracken_report.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"name": "Enterococcus_faecalis", "taxonomy_id": 1351, "taxonomy_lvl": "S", "kraken_assigned_reads": 63, "added_reads": 21, "new_est_reads": 84, "fraction_total_reads": 0.88421}, {"name": "Enterococcus_faecium", "taxonomy_id": 1352, "taxonomy_lvl": "S", "kraken_assigned_reads": 4, "added_reads": 0, "new_est_reads": 4, "fraction_total_reads": 0.04211}, {"name": "Enterococcus_casseliflavus", "taxonomy_id": 37734, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, {"name": "Streptococcus_cristatus", "taxonomy_id": 45634, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, {"name": "Lactococcus_garvieae", "taxonomy_id": 1363, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, {"name": "Staphylococcus_aureus", "taxonomy_id": 1280, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, {"name": "Bacillus_oleronius", "taxonomy_id": 38875, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, {"level": "S", "threshold": "0.1", "read_len": "100"}]}, {"name": "kraken_report", "file_path": "tests/data/dummy/bracken/bracken_kraken_report.tsv", "hid": "12345", "content": [{"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "R", "ncbi_taxonomic_id": 1, "scientific_name": "root"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "R1", "ncbi_taxonomic_id": 131567, "scientific_name": "cellular_organisms"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "D", "ncbi_taxonomic_id": 2, "scientific_name": "Bacteria"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "D1", "ncbi_taxonomic_id": 1783272, "scientific_name": "Terrabacteria_group"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "P", "ncbi_taxonomic_id": 1239, "scientific_name": "Firmicutes"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "C", "ncbi_taxonomic_id": 91061, "scientific_name": "Bacilli"}, {"fragment_coverage": 97.87, "fragment_number": 92, "assigned_fragment_number": 0, "rank_code": "O", "ncbi_taxonomic_id": 186826, "scientific_name": "Lactobacillales"}, {"fragment_coverage": 95.16, "fragment_number": 90, "assigned_fragment_number": 0, "rank_code": "F", "ncbi_taxonomic_id": 81852, "scientific_name": "Enterococcaceae"}, {"fragment_coverage": 95.16, "fragment_number": 90, "assigned_fragment_number": 0, "rank_code": "G", "ncbi_taxonomic_id": 1350, "scientific_name": "Enterococcus"}, {"fragment_coverage": 89.01, "fragment_number": 84, "assigned_fragment_number": 84, "rank_code": "S", "ncbi_taxonomic_id": 1351, "scientific_name": "Enterococcus_faecalis"}, {"fragment_coverage": 4.89, "fragment_number": 4, "assigned_fragment_number": 4, "rank_code": "S", "ncbi_taxonomic_id": 1352, "scientific_name": "Enterococcus_faecium"}, {"fragment_coverage": 1.25, "fragment_number": 1, "assigned_fragment_number": 1, "rank_code": "S", "ncbi_taxonomic_id": 37734, "scientific_name": "Enterococcus_casseliflavus"}, {"fragment_coverage": 2.71, "fragment_number": 2, "assigned_fragment_number": 0, "rank_code": "F", "ncbi_taxonomic_id": 1300, "scientific_name": "Streptococcaceae"}, {"fragment_coverage": 1.63, "fragment_number": 1, "assigned_fragment_number": 0, "rank_code": "G", "ncbi_taxonomic_id": 1301, "scientific_name": "Streptococcus"}, {"fragment_coverage": 1.63, "fragment_number": 1, "assigned_fragment_number": 1, "rank_code": "S", "ncbi_taxonomic_id": 45634, "scientific_name": "Streptococcus_cristatus"}, {"fragment_coverage": 1.08, "fragment_number": 1, "assigned_fragment_number": 0, "rank_code": "G", "ncbi_taxonomic_id": 1357, "scientific_name": "Lactococcus"}, {"fragment_coverage": 1.08, "fragment_number": 1, "assigned_fragment_number": 1, "rank_code": "S", "ncbi_taxonomic_id": 1363, "scientific_name": "Lactococcus_garvieae"}, {"fragment_coverage": 2.13, "fragment_number": 2, "assigned_fragment_number": 0, "rank_code": "O", "ncbi_taxonomic_id": 1385, "scientific_name": "Bacillales"}, {"fragment_coverage": 1.08, "fragment_number": 1, "assigned_fragment_number": 0, "rank_code": "F", "ncbi_taxonomic_id": 90964, "scientific_name": "Staphylococcaceae"}, {"fragment_coverage": 1.08, "fragment_number": 1, "assigned_fragment_number": 0, "rank_code": "G", "ncbi_taxonomic_id": 1279, "scientific_name": "Staphylococcus"}, {"fragment_coverage": 1.08, "fragment_number": 1, "assigned_fragment_number": 1, "rank_code": "S", "ncbi_taxonomic_id": 1280, "scientific_name": "Staphylococcus_aureus"}, {"fragment_coverage": 1.05, "fragment_number": 1, "assigned_fragment_number": 0, "rank_code": "F", "ncbi_taxonomic_id": 186817, "scientific_name": "Bacillaceae"}, {"fragment_coverage": 1.05, "fragment_number": 1, "assigned_fragment_number": 0, "rank_code": "G", "ncbi_taxonomic_id": 1386, "scientific_name": "Bacillus"}, {"fragment_coverage": 1.05, "fragment_number": 1, "assigned_fragment_number": 1, "rank_code": "S", "ncbi_taxonomic_id": 38875, "scientific_name": "Bacillus_oleronius"}]}], "tool_has_database": true}]