| Previous changeset 2:def7a82d23e1 (2024-07-03) Next changeset 4:24eec94e6dfc (2024-10-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 4225d0fe8f224f56ec8066c705e56f4e8c1d9a9a |
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modified:
macro.xml |
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removed:
test-data/summarize/amrfinderplus_output.json test-data/summarize/bakta_all_output.json test-data/summarize/bandage_output.json test-data/summarize/bwa_output.json test-data/summarize/fastp_output.json test-data/summarize/fastqc_output.json test-data/summarize/filtlong_output.json test-data/summarize/flye_output.json test-data/summarize/integronfinder2_output.json test-data/summarize/isescan_output.json test-data/summarize/kraken2_output.json test-data/summarize/multiqc_output.json test-data/summarize/polypolish_output.json test-data/summarize/quast_output.json test-data/summarize/recentrifuge_output.json test-data/summarize/refseqmasher_output.json test-data/summarize/shovill_output.json test-data/summarize/staramr_output.json test-data/summarize/tabular_file_output.json |
| b |
| diff -r def7a82d23e1 -r f3233d395549 macro.xml --- a/macro.xml Wed Jul 03 12:07:36 2024 +0000 +++ b/macro.xml Mon Sep 30 10:16:31 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.9</token> + <token name="@TOOL_VERSION@">0.9.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/amrfinderplus_output.json --- a/test-data/summarize/amrfinderplus_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "3.11.26", "reference_database_version": "v3.11-2023-04-17.1", "analysis_software_name": "amrfinderplus", "results": [{"name": "amrfinderplus_report", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_report.tsv", "hid": "12345", "galaxy_id": null, "content": [{"Protein identifier": null, "Contig id": "contig_153_polypolish", "Start": 4412, "Stop": 4645, "Strand": "-", "Gene symbol": "merE", "Sequence name": "broad-spectrum mercury transporter MerE", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "BLASTX", "Target length": 78, "Reference sequence length": 78, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 96.15, "Alignment length": 78, "Accession of closest sequence": "AAC38236.1", "Name of closest sequence": "broad-spectrum mercury transporter MerE", "HMM id": null, "HMM description": null, "Hierarchy node": "merE"}, {"Protein identifier": null, "Contig id": "contig_153_polypolish", "Start": 7613, "Stop": 7846, "Strand": "-", "Gene symbol": "merT", "Sequence name": "mercuric transport protein MerT", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "PARTIALX", "Target length": 78, "Reference sequence length": 116, "% Coverage of reference sequence": 67.24, "% Identity to reference sequence": 92.31, "Alignment length": 78, "Accession of closest sequence": "CAA70196.1", "Name of closest sequence": "mercuric transport protein MerT", "HMM id": null, "HMM description": null, "Hierarchy node": "merT"}, {"Protein identifier": null, "Contig id": "contig_160_polypolish", "Start": 86415, "Stop": 86654, "Strand": "-", "Gene symbol": "fosA", "Sequence name": "FosA5 family fosfomycin resistance glutathione transferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "FOSFOMYCIN", "Subclass": "FOSFOMYCIN", "Method": "PARTIALX", "Target length": 80, "Reference sequence length": 139, "% Coverage of reference sequence": 57.55, "% Identity to reference sequence": 98.75, "Alignment length": 80, "Accession of closest sequence": "WP_114473955.1", "Name of closest sequence": "fosfomycin resistance glutathione transferase FosA9", "HMM id": null, "HMM description": null, "Hierarchy node": "fosA5_fam"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 3018, "Stop": 3344, "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "PARTIALX", "Target length": 109, "Reference sequence length": 144, "% Coverage of reference sequence": 75.69, "% Identity to reference sequence": 93.58, "Alignment length": 109, "Accession of closest sequence": "BAA20334.1", "Name of closest sequence": "mercury resistance transcriptional regulator MerR", "HMM id": null, "HMM description": null, "Hierarchy node": "merR_Ps"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 5821, "Stop": 6243, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "PARTIALX", "Target length": 141, "Reference sequence length": 219, "% Coverage of reference sequence": 64.38, "% Identity to reference sequence": 98.58, "Alignment length": 141, "Accession of closest sequence": "WP_000412211.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 5821, "Stop": 6243, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope":'..b'ol": "dfrA30", "Sequence name": "trimethoprim-resistant dihydrofolate reductase DfrA30", "Length": 318, "Sequence": "GGGGCGCTCCCCAATAGGAAATACGCGGTCGTTACTCGCTCAGCTCGGACGGCCAATAATGACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCACCGGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCTACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATTCCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGT"}, {"Name": "contig_40_polypolish:2574-3359", "Contig id": "contig_40_polypolish", "Start": "2574", "Stop": "3359", "Strand": "+", "Gene symbol": "aph(3\'\')-Ib", "Sequence name": "aminoglycoside O-phosphotransferase APH(3\'\')-Ib", "Length": 786, "Sequence": "ATATTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGATTTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGCGGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGCCCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATTCCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATGGGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGTTTGAGCGCAGGCTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGACTTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGAGAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCCTGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTTGGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAAGAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTGGGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACTTGGGGT"}, {"Name": "contig_40_polypolish:3555-4103", "Contig id": "contig_40_polypolish", "Start": "3555", "Stop": "4103", "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Length": 549, "Sequence": "GGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAGCGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCGAGCGACCGAAATTGCAGCGGAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCGATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGTCAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAACTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGGCTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTCTACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCGGACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCGTGCGTACGCTTATGGGTGC"}, {"Name": "contig_40_polypolish:632-1258", "Contig id": "contig_40_polypolish", "Start": "632", "Stop": "1258", "Strand": "+", "Gene symbol": "aph(3\')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3\')-Ia", "Length": 627, "Sequence": "ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACATGGATGCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCGATCCCCGGGAAAACAGCATTCCGGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCTTTTAACAACGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTTGACGAGGGA"}, {"Name": "contig_41_polypolish:100023-100541", "Contig id": "contig_41_polypolish", "Start": "100023", "Stop": "100541", "Strand": "-", "Gene symbol": "terD", "Sequence name": "tellurium resistance membrane protein TerD", "Length": 519, "Sequence": "ATGAGCGTTTCACTATCTAAAGGCGGCAACGTTTCCCTGAGCAAAACCGCGCCAAGCATGAAAAACGTGCTGGTTGGCCTTGGCTGGGATGCACGTTCTACGGACGGTCAGGACTTTGACCTCGATGCTTCCGCATTTCTGCTGGCAGCCAATGGCAAGGTTCGTGGCGATGCAGATTTCATTTTCTATAACAACCTGAAATCTGCTGATGGTTCCGTTACTCATACCGGTGATAACCGTACCGGTGAAGGTGATGGCGACGATGAATCCCTCAAAATCAAACTGGACGCGGTACACGGGGATGTCGACAAAATTATTTTCGTTGTCACTATCCATGATGCTCAGGCTCGTCGCCAGAGCTTCGGTCAGGTTTCCGGCGCATTTATCCGTCTGGTGAATGATGACAATCAGACTGAAGTTGCTCGCTACGATCTGACAGAAGACGCTTCTACTGAAACTGCCATGCTGTTTGGGGAGCTGTATCGTCACAACGGAGAATGGAAATTCCGTGCGGTTGGC"}]}], "tool_has_database": true}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/bakta_all_output.json --- a/test-data/summarize/bakta_all_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_version": "1.8.1", "reference_database_version": "5.0", "analysis_software_name": "bakta", "results": [{"name": "bakta_report", "file_path": "tests/data/dummy/bakta/bakta.json", "hid": "12345", "galaxy_id": null, "content": [{"genome": {"genus": null, "species": null, "strain": null, "complete": true, "gram": "?", "translation_table": 11}, "stats": {"no_sequences": 1, "size": 1330, "gc": 0.4518796992481203, "n_ratio": 0.0, "n50": 1330, "coding_ratio": 0.6203007518796992}, "features": [{"type": "cds", "contig": "contig_1", "start": 413, "stop": 736, "strand": "+", "frame": 2, "gene": null, "product": "hypothetical protein", "db_xrefs": [], "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", "start_type": "ATG", "rbs_motif": "GGAG/GAGG", "hypothetical": true, "genes": [], "seq_stats": {"molecular_weight": 12072.9082, "isoelectric_point": 10.3678861618}, "id": "IHHALPPJCH_1", "locus": "IHHALP_00005", "edge": null}, {"type": "cds", "contig": "contig_1", "start": 971, "stop": 141, "strand": "-", "frame": 1, "gene": null, "product": "hypothetical protein", "db_xrefs": [], "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", "start_type": "ATG", "rbs_motif": "AGGA/GGAG/GAGG", "hypothetical": true, "genes": [], "seq_stats": {"molecular_weight": 18866.3258, "isoelectric_point": 7.6965906143}, "id": "IHHALPPJCH_2", "locus": "IHHALP_00010", "edge": true}], "run": {"start": "2024-02-11 00:24:53", "end": "2024-02-11 00:25:06"}, "summary": {"tRNAs": 0, "tmRNAs": 0, "rRNAs": 0, "ncRNAs": 0, "ncRNAregions": 0, "CRISPRarrays": 0, "CDSs": 2, "pseudogenes": 0, "hypotheticals": 2, "signalpeptides": 0, "sORFs": 0, "gaps": 0, "oriCs": 0, "oriVs": 0, "oriTs": 0}}]}, {"name": "annotation_tabular_path", "file_path": "tests/data/dummy/bakta/bakta_annotation.tsv", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "gff_file_path", "file_path": "tests/data/dummy/bakta/bakta_annotation.gff3", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "annotation_genbank_path", "file_path": "tests/data/dummy/bakta/bakta_gbff.gbff", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "annotation_embl_path", "file_path": "tests/data/dummy/bakta/bakta_embl.embl", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "contig_sequences_path", "file_path": "tests/data/dummy/bakta/bakta_contigs_sequences.fna", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "nucleotide_annotation_path", "file_path": "tests/data/dummy/bakta/bakta_nucleotide_annotation.ffn", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "amino_acid_annotation_path", "file_path": "tests/data/dummy/bakta/bakta_aminoacid.faa", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "hypothetical_protein_path", "file_path": "tests/data/dummy/bakta/bakta_hypothetical.faa", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "hypothetical_tabular_path", "file_path": "tests/data/dummy/bakta/bakta_hypothetical.tsv", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "summary_result_path", "file_path": "tests/data/dummy/bakta/bakta_summary.txt", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "plot_file_path", "file_path": "tests/data/dummy/bakta/bakta_plot.svg", "hid": "98765", "galaxy_id": null, "content": []}], "tool_has_database": true}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/bandage_output.json --- a/test-data/summarize/bandage_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_version": "1.0", "reference_database_version": "", "analysis_software_name": "bandage", "results": [{"name": "bandage_report", "file_path": "tests/data/dummy/bandage/bandage_info.txt", "hid": "12345", "galaxy_hid": "", "content": {"Node_count": "222", "Edge_count": "299", "Smallest_edge_overlap_(bp)": "127", "Largest_edge_overlap_(bp)": "127", "Total_length_(bp)": "3042326", "Total_length_no_overlaps_(bp)": "3014132", "Dead_ends": "0", "Percentage_dead_ends": "0%", "Connected_components": "2", "Largest_component_(bp)": "3042198", "Total_length_orphaned_nodes_(bp)": "3042198", "N50_(bp)": "79920", "Shortest_node_(bp)": "128", "Lower_quartile_node_(bp)": "151", "Median_node_(bp)": "256", "Upper_quartile_node_(bp)": "7566", "Longest_node_(bp)": "239204", "Median_depth": "22.997", "Estimated_sequence_length_(bp)": "3234717"}}, {"name": "bandage_plot_path", "file_path": "tests/data/dummy/bandage/bandage_plot.svg", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/bwa_output.json --- a/test-data/summarize/bwa_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_version": "2.2.1", "reference_database_version": "tests/data/dummy/flye/assembly.fasta", "analysis_software_name": "bwa", "results": [{"name": "bwa_report", "file_path": "tests/data/dummy/bwa/aligned_R1.bam", "hid": "12345", "galaxy_id": null, "content": []}, {"name": "paired_second_file_path", "file_path": "tests/data/dummy/bwa/aligned_R2.bam", "hid": "12345", "galaxy_id": null, "content": []}], "tool_has_database": true}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/fastp_output.json --- a/test-data/summarize/fastp_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "0.23.2", "reference_database_version": "", "analysis_software_name": "fastp", "results": [{"name": "fastp_report", "file_path": "tests/data/dummy/fastp/fastp_report.json", "hid": "12345", "galaxy_hid": "", "content": {"summary": {"sequencing": "paired end (301 cycles + 301 cycles)", "before_filtering": {"total_reads": 3489582, "total_bases": 705053822, "q20_bases": 672633294, "q30_bases": 625189177, "q20_rate": 0.954017, "q30_rate": 0.886725, "read1_mean_length": 201, "read2_mean_length": 202, "gc_content": 0.374995}, "after_filtering": {"total_reads": 3440258, "total_bases": 690189367, "q20_bases": 665469579, "q30_bases": 620744461, "q20_rate": 0.964184, "q30_rate": 0.899383, "read1_mean_length": 200, "read2_mean_length": 200, "gc_content": 0.374878}}, "filtering_result": {"passed_filter_reads": 3440258, "corrected_reads": 464332, "corrected_bases": 996846, "low_quality_reads": 49324, "too_many_N_reads": 0, "too_short_reads": 0, "too_long_reads": 0}, "duplication": {"rate": 0.0185954}, "insert_size": {"peak": 147, "unknown": 18596, "histogram": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 528, 88, 57, 60, 72, 95, 143, 159, 219, 267, 229, 179, 112, 111, 111, 178, 221, 273, 276, 358, 350, 296, 199, 163, 192, 231, 347, 432, 475, 491, 524, 385, 336, 252, 243, 325, 382, 502, 628, 650, 631, 582, 541, 420, 386, 377, 523, 624, 753, 847, 852, 804, 641, 555, 490, 473, 624, 763, 923, 961, 1057, 972, 858, 740, 657, 609, 670, 847, 1038, 1182, 1254, 1208, 1139, 995, 831, 783, 782, 991, 1065, 1327, 1443, 1450, 1258, 1115, 1013, 901, 901, 1046, 1190, 1299, 1488, 1510, 1511, 1321, 1132, 1065, 1060, 1098, 1242, 1355, 1454, 1609, 1527, 1472, 1305, 1184, 1055, 1113, 1203, 1312, 1498, 1496, 1628, 1481, 1364, 1273, 1142, 1166, 1209, 1299, 1455, 1513, 1533, 1457, 1435, 1340, 1168, 1155, 1160, 1324, 1341, 1438, 1506, 1554, 1357, 1306, 1241, 1147, 1112, 1257, 1308, 1353, 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298, 284, 278, 272, 275, 253, 230, 249, 241, 249, 257, 282, 264, 257, 243, 238, 248, 262, 227, 215, 261, 260, 240, 221, 246, 253, 227, 223, 194, 246, 245, 227, 235, 207, 228, 209, 197, 239, 205, 189, 189, 217, 185, 197, 211, 179, 190, 212, 180, 178, 182, 171, 190, 196, 192, 174, 202, 162, 167, 169, 170, 162, 162, 169, 162, 145, 160, 141, 175, 165, 160, 151, 161, 151, 166, 148, 151, 124, 169, 148, 144, 138, 137, 143, 156, 153, 130, 140, 165, 149, 130, 170, 150, 114, 130, 129, 129, 134, 121, 117, 127, 125, 124, 115, 117, 134, 127, 128, 107, 129, 115, 135, 106, 112, 100, 117, 121, 113, 104, 106, 112, 101, 96, 112, 102, 96, 126, 90, 111, 106, 97, 109, 121, 99, 89, 111, 81, 104, 95, 96, 97, 93]}, "adapter_cutting": {"adapter_trimmed_reads": 75904, "adapter_trimmed_bases": 2561055, "read1_adapter_sequence": "unspecified", "read2_adapter_sequence": "unspecified", "read1_adapter_counts": {"C": 292, "CTG": 108, "CTT": 147, "CTGG": 56, "CTGTC": 815, "CTGTCTC": 118, "others": 3652}, 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63212, "GCGGA": 169615, "GCGGT": 174750, "GCGGC": 159727, "GCGGG": 91200, "GGAAA": 572492, "GGAAT": 411350, "GGAAC": 282731, "GGAAG": 262988, "GGATA": 268641, "GGATT": 429098, "GGATC": 154559, "GGATG": 202465, "GGACA": 203164, "GGACT": 146635, "GGACC": 100589, "GGACG": 125871, "GGAGA": 175926, "GGAGT": 118343, "GGAGC": 121295, "GGAGG": 112157, "GGTAA": 346420, "GGTAT": 231611, "GGTAC": 164801, "GGTAG": 147299, "GGTTA": 269807, "GGTTT": 463440, "GGTTC": 253317, "GGTTG": 272685, "GGTCA": 201814, "GGTCT": 130918, "GGTCC": 101230, "GGTCG": 125540, "GGTGA": 241660, "GGTGT": 231666, "GGTGC": 183585, "GGTGG": 211260, "GGCAA": 380065, "GGCAT": 253024, "GGCAC": 167326, "GGCAG": 159044, "GGCTA": 213608, "GGCTT": 360565, "GGCTC": 117871, "GGCTG": 187686, "GGCCA": 155497, "GGCCT": 88425, "GGCCC": 58580, "GGCCG": 81779, "GGCGA": 199113, "GGCGT": 188685, "GGCGC": 152509, "GGCGG": 151043, "GGGAA": 269835, "GGGAT": 217695, "GGGAC": 106953, "GGGAG": 73751, "GGGTA": 107585, "GGGTT": 169248, "GGGTC": 77547, "GGGTG": 90238, "GGGCA": 134473, "GGGCT": 112465, "GGGCC": 58310, "GGGCG": 93397, "GGGGA": 135255, "GGGGT": 85222, "GGGGC": 89825, "GGGGG": 54021}, "overrepresented_sequences": {}}, "command": "fastp --thread 6 --report_title fastp_report --compression 4 --html ./report.html --json ./report.json -i /home/pierre/Seafile/ABROMICS_IFB/genome_test_CNR/fastq/10_Enterococcus_faecalis_S17_L001_R1_001.fastq.gz -I /home/pierre/Seafile/ABROMICS_IFB/genome_test_CNR/fastq/10_Enterococcus_faecalis_S17_L001_R2_001.fastq.gz --detect_adapter_for_pe -q 15 -c "}}, {"name": "trimmed_forward_R1_path", "file_path": "tests/data/dummy/fastp/trimmed_R1.fastq.gz", "hid": "12345", "galaxy_id": "", "content": {}}, {"name": "trimmed_reverse_R2_path", "file_path": "tests/data/dummy/fastp/trimmed_R2.fastq.gz", "hid": "12345", "galaxy_id": "", "content": {}}, {"name": "html_report_path", "file_path": "tests/data/dummy/fastp/fastp_report.html", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/fastqc_output.json --- a/test-data/summarize/fastqc_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "0.12.1", "reference_database_version": null, "analysis_software_name": "fastqc", "results": [{"name": "fastqc_report", "file_path": "tests/data/dummy/fastqc/fastqc_report.txt", "hid": "12345", "galaxy_id": null, "content": [{"basic_statistics": [{"Measure": "Filename", "Value": "SRR8335315_150M_fastq"}, {"Measure": "File type", "Value": "Conventional base calls"}, {"Measure": "Encoding", "Value": "Sanger / Illumina 1.9"}, {"Measure": "Total Sequences", "Value": "150000"}, {"Measure": "Total Bases", "Value": "1 Gbp"}, {"Measure": "Sequences flagged as poor quality", "Value": "0"}, {"Measure": "Sequence length", "Value": "5000-208721"}, {"Measure": "%GC", "Value": "49"}], "per_base_sequence_quality": [{"Base": "1", "Mean": 2.8365066666666667, "Median": 2.0, "Lower Quartile": 1.0, "Upper Quartile": 4.0, "10th Percentile": 1.0, "90th Percentile": 6.0}, {"Base": "2", "Mean": 5.008253333333333, "Median": 3.0, "Lower Quartile": 2.0, "Upper 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"Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "165000-169999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "170000-174999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "175000-179999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "180000-184999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "185000-189999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "190000-194999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "195000-199999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "200000-204999", "Illumina Universal Adapter": 0.025999999999999, "Illumina Small RNA 3\' Adapter": 0.0306666666666639, "Illumina Small RNA 5\' Adapter": 0.0153333333333319, "Nextera Transposase Sequence": 0.0913333333333398, "PolyA": 1.825999999999928, "PolyG": 0.1286666666666609}, {"Position": "205000-208710", "Illumina Universal Adapter": 0.0259999999999997, "Illumina Small RNA 3\' Adapter": 0.0306666666666647, "Illumina Small RNA 5\' Adapter": 0.0153333333333323, "Nextera Transposase Sequence": 0.0913333333333354, "PolyA": 1.8260000000000205, "PolyG": 0.1286666666666718}]}]}, {"name": "html_report_path", "file_path": "tests/data/dummy/fastqc/fastqc_report.html", "hid": "12345", "galaxy_id": null, "content": []}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/filtlong_output.json --- a/test-data/summarize/filtlong_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_version": "0.2.1", "reference_database_version": null, "analysis_software_name": "filtlong", "results": [{"name": "filtlong_report", "file_path": "tests/data/dummy/filtlong/filtered_sample.fastq.gz", "hid": "12345", "galaxy_id": null, "content": []}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/flye_output.json --- a/test-data/summarize/flye_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "2.9.1", "reference_database_version": null, "analysis_software_name": "flye", "results": [{"name": "flye_report", "file_path": "tests/data/dummy/flye/assembly.fasta", "hid": "12345", "galaxy_id": null, "content": [{"name": "contig_1", "length": 6770, "sequence": "AGTTTTTTGTGTGTTGTTTTATTGTTTTGCGTGGTTTGTTTTTATTGTTATTTCATTAAGGAAGGTAAATTCAGGATGGCAGTCTGTAGATAATCGGAGGTCACTTATGCTACATGATCACGTGGCAGAATGTCTGGAGAAAAAGGACTGTACCGGAGAGCAGCTGAACGATGGGCAAAAGTGATGGTACAGCTAAGTGATGACCAGAAAGAAAAGTGGCGGCACAGAAACGAGCAGAGTGTTTGCGTAAGGCGCGCGGACTCCGGTTTCACCGGTGAACCTGACCGAAATAAAACAAGCGGTCAACAGACTACATTCTGAGTTGGGAATGGATTTGAAGAGCGGCGGGTATTCCGACGATATAAAGGGACAGGAGAACAGAATACGTCCGGAAACGCGCGGTCAAAAAATGCTAAAAATATCTGAGAGAGTTATTGCCTGTTACCATAAGAAAAAGCGACTTTAGTGGTCGCTTTTGTGTCATATATAAGTCGTTTAAGTAAACCTGTCTGAACAGGTGCTCTGGTCGTGTTTGTCTTTGTTGGGTACAAATTGAGAATATTTTCATTAATTAATCTTCTTCTGCAGGCTTCAATAACCCACGCTGAAAAATTACCTGAACCTTTCAGGTCAAGAGCGATGTTAATTTGTTCAATTATCTGGTTTGGAAATCGGATGTTGCGGGTTGTTGTTCTGCGGGTTCTGTTCTTTGATGACATAATGTTGCCCCGTATTCAGTGTTGCTGATTTGTATTATCTGAAGTTGCTTTTACGCTAATTTGATGCAGATCAATTAATACGATACCTGCGTAATAATTGATTATTTCTCGTGGTTTGATGGCGTACACATGTCGTGATAAACCTCATGTAGATGATAATTATTATCATTTTCGTGGGTCCTTTCCGGCGATCCGACAGGTTACGGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGTGTTTCCGTTCTTCTTCGTCGTAACTTAATGTTTTATTTAAAATACCCCTGAAAGAAAGGAAACGACAGGTGCTGAAAACGGGCTTTTGGCCTCTGTCGTTTCCTTTCTCTGTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGATTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAGCTGCGCCGGGAAGTTGAAGAACTGCGGCAGGCCAGCGAGACAGATCTCCAGCCGGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAGCTGAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCCAGTTACTATCTCCCGAAAGAATCCGCATACCGTGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGCGAGGTGAATGTGGTGAAGTCTGCCCGTGTTGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTACTTCATAGAGCATAAGCAGCGCAACACACTTATCTGGTTGCCGACGGATGGTGATGCCGAGAACTTTATGAAAACCCACGTTGAGCCGACCATCCGCGATATTCCGTCGCTGCTGGCGCTGGCTCCGTGGTATGGCAAAAGCACCGGGATAACACGCTCACTATGAAGCGTTTTTCCAATGGTCGTGGCTTCTGGTGCCCGGGCGGTAAAGCGGCAAAAACTACCGTGAAAAGTCGGTGGATGTGGCGGGTTATGATGAACTTGCTGCCTTTGATGAGGATATTGAACAGGAAGGCTCTCCGACGTTCTCGGGCGATAAGCGTATTGAAGGCTCGGTCTGGCCAAAGTCCATCCGTGGCTCCACGCCCAAAGTGAGAGCACCTGCCAGATTGAGCGTGCAGCCAGTGAATCCCGCATTTTATGCGTTTTCATGTTGCCTGCCCGCACTGCGGGAGGAGCAGTATCTTAAATTTGGCGACAAAGAGACGCCGTTTGGCCTCAAATGGACGCCGGATGACCCTCCAGCGTGTTTTATCTCTGCGAGCATAATGCCTGCGTCATCCGCCAGCAGGAGCTGGACTTTACTGATGCCCGTTATATCTGCGAAAAGACCGGGATCTGGACCCGTGATGGCATTCTCTGGTTTCGTCATCCGGTGAAGAGATTGAACCGCCTGACAGTGTGACCTTTCACATCTGGACGGCGTACAGCCCGTTCACCACGGGTGCAGATTGTCAAAGACTGGATGAAGACGAAAGGGATACGGGAAAACGTAAAACCTTCGTGAACACCACGCTCGGTGAGACGTGGGAAGCGAAAATCGGCGAACGTCCGGATGCTGAGGTGATGGCGGAGCGGAAGAGTATTATTCAGCGCCCGTTCCTGATCGTGTGGCTTACCTGACCGCCGGTATCGACTCCCAGCTGGACCGCTACGAAATGCGCGTATGGGGATGGGGGCCGGGTGAGAAAGCTGGCTGATTGACCGGCAGATTATTATGGGCCGCCACGACGATGAACAGACGCTGCTGCGTGGATGAGGCCATCAATAAAACCTATACCCGCCGGAATGGTGCAGAAATGTCGGTATCCCGTATCTGCTGGGATACTGGCGGGATTGACCCGACCATTGTGTATGAACGCTCGAAAAACATGGGCTGTTCCGGGTGATCCCATTAAAGGGCATCCGTCTACGGAAAGCCGGTGGCCAGCATGCCACGTAAGCGAAACAAAACGGGTTTACCTTACCGAAATCGGTACGGATACCGCGAAAGAGCAGATTTATAACCGCTTCACACTGACGCCGGAAGGGATGAACCGCTTCCGGTGCCGTTCACTTCCGAATAACCCGGATATTTTGATCTTACCGAAGCGCAGCAACTGACTGCTGAAGAGCAGGTCGAAAAATGGGTGGATGGCAGGAAAAAATACTGTGGGACAGCAAAAGCGACGCAATGAGGCGCTCGACTGCTTCGTTTATGCGCTGGCGGCGCTGCGCATCAGTATTTCCGCTGGCAGCTGGATCTCAGTGCACTGCTGGCGAGCCTGCAGGAAGAGGATGGTGCAGCAACCAACAAGAAAACACTGGCAGAATACGCCCGTGCCTTATCCGGAGAGGATGAATGACGCGACAGGAAGAACTTGCCGCTGCCCGTGCGGCACTGCATGACCTGATGACAGGAAAACGGGTGGCAACGGTACAGAAAGACGGACGGCGAGTGGGTTTACGACCACTTCCGTGTCTGACCTGAAAAATACATTGCTGAGCTGGAAGTGCAGACCGGCATGAC'..b'TGCCGGGGACTCACTGAACCTGCAGACGGCTCAGGACACGGATAACGGCTACTCCGTGTTTGAGCAGTCACTGCTGCGGTATATCGCTGCCGGGCTGGGTGTCTCGTATGAGCAGCTTTCCGGAATTACGCCCAGATGAGCTACTCCACGGCACGGGCCAGTGCGAACGAGTCGTGGGCGTACTTTATGGGGCGGCGAAAATTCGTCGCATCCCGTCAGGCGAGCCAGATGTTTCTGTGCTGGCTGGAAGAGGCCATCGTTCGCCGCGTGGTGACGTTACCTTCAAAAGCGCGCTTCAGCTTTCAGGAAGCCCGCAGTGCTCGGGGAACTGCGACTGGATAAGCTCGGTCGTATGGCCATCGATGGTCTGAAGAAGTTCAGGAAGCGGTGATGCTGATAGAAGCCGGACTGAGCACCTACGAGAAAGTGCGCGAAACGCGGTGACGACTATCAGGAAATTTTGCCCAGCAGGTCCGTGAAACGATGGAGCGCCGCGCAGCTGGTCTTAAACCGCCCGCACGGGCGGCTGCGGCATTGAATCCGGGCTGCGACAATCAACAGAGGAGGAGAAGAGTGACAGCAGAGCTGCGTAATCTCCCGCATATTGCCAGCATGGCTTTTAATGAGCCGCTGATGCTTGAACCCGCCTATGCGCGGGTTTTCTTTGTGCGCTTGCAGGCCAGCTTGGGATCAGCCGCCTGACGGATGCAGTATCCGGCGACAGCCTGACTGCCGGAGAGGCACCCGCGGCGCTGGCGTTATCCGGTGATGATGACGGACCACGACAGGCCCGGAGTTATCAGGTCATGAACGGCATCGCCGTGCTGCCGGTGTCCGGTACGCTGGTCAGCCGGACGCGGGCGCTGCAGCCGTATTCGGGAATGACCGGTTACAACGGCATTATCGCCCGTCTGCAACAGGCTGCCAGCGATCCGATGGTGGACGGCATTCTGCTCGATATGGACACACCGGGCGGGATGGTGGCGGGAGCATTTGACTGTGCTGACATCATCGCCCGTGTGCGAGACATCAAACCGGTATGGGCGCTGGCCAACGACATGAACTGCAGTGCAGGTCAGCTGCTTGCCAGCGCCGCCTCCCGGCGTCTGGTCACGCAGACCGCCCGGACAGGCTCCATCGGCGTCATGATGGCTCACAGTAATTACGGTGCTGCCTCGGAGAAACAGGGCGTGAAATCACGCTGATTTACAGCGGCAGCCATAAGGTGGATGGCAACCCTACAGCCATCTACCGGGTGATGTCCGGAAACACTGCAGTCCCGGATGGATGCAACCCGCCGGATGTTTGCGCAGAAGGTGTCGGCATATACCGGCCTGTCCGTGCAGGCTGTGCTGGATACCGAGGCTGCAGTGTACAGCGGTCAGGAGGCCATTGATGCCGGACTGGCTGATGAACTTGTCAACAGCACCGATGCGATCACCGTTATGCGTGATGCACTGGATGCACGTAAATCCGTCTCTCAGGAGGGCGAATGACCAAAGAGACTCAATCAACAACTGTTTCAGCCACTGCTTCGCAGGCTGACGTTACTGGCGTGGTGCCAGCGACGGAGGGCGAAAACGCCAGCGCGGCGCAGCCGGACGTGAACGCGCAGATCACCGCTGCGGTTGCGGCAGAAAACAGCCGCATTATGGGGATCCTCAACTGTGAGGAGGCTCACGGACGCGAAGAACAGGCCCGCGTGCTGGCAGAAACCCCGGTATGACCGTGGAAACGGCCCGCCGCATTCTGGCCGCAGCACCACAGAGTGCACAGGCGCGCAGTGATACTGCGCTGGATCGTCTGATGCAGGGGCACCGGCACCGCTGGCTGCAGGTAACCGGCATCTGATGCCGTTAACGATTTGCTGAACACACCAGTGTAAGGGATGTTTATGACGAGCAAAGAAACCTTTACCCATTACCAGCCGCTGGGCAACAGTGACCCGGCTCATACCGCAACCGCGCCCGGCGGATTGAGTGCGAAAGCGTCTGCAATGACCCCGCTGATGCTGGACACCGCCACCCGTAAGCTGGTTGCGTGGGATGGCACCACCGACGG"}, {"name": "contig_2", "length": 720, "sequence": "CCATGGTGTAATCACCAATATTTTTCATTTTATCAACGGGTTTAGTTGATTAGTTGTAGTACCTGTACCGCTCAGATAAGTAGCTGTCCAGTTAGTCATTCTTGTTAGGTTAAATCCTATCAGTTTTAAGATTGCTGATTGAGGATCTTGAGTATTAGATGCCCGTATTCACTGGCTGAGGTGGCTGTTCCCAGTGCAGGTGTATATGGTGAGTTTTGCAACTGTGCACGGTAAGCTCCTTTTACTTCCTTCAGAATTCAGTATCCCTGCTTCGCCCTGCGATGAAACTCCACTCACAGTGGGGCACGGTCGGCCAGTTCTGCCAGTCGCTGGTTGGCAGTGGCAAAGGTCTGGTACCGAGCCCCGAGGCAACCCAGCCGTAGGTGGTCAGGTAGGATTTCAGCTGCTCCTGCGCTCAGTTTCTGCGTTATCTGTTGGCAACGCCTTCTGCACCGTTTCTTCATACCTGTTGGCAGCCTTCTGAATACGGCTTTCAATATCCGGCAGGTTGCCGTTACCCGTGTCGCGTCGGGTCCGGTACGCTGACACAAATTCCTGTGCTGCGCTGTCCGGTCACGGAGCATGGTATCCATGGCGGAGCGTTGTGCCGTCAGGACACCCTGATACTCCGTTTCAATGAAGGGATTGAAAAAATAGTCCAGTGCGGACTGGTTGTTGCTGCCATTCCTTTCACGGTGAGACTCACACTCCCGCAGGTGG"}]}, {"name": "assembly_infos", "file_path": "tests/data/dummy/flye/assembly_infos.tsv", "hid": "12345", "galaxy_id": null, "content": [{"#seq_name": "contig_2", "length": 4031962, "cov.": 189, "circ.": "N", "repeat": "N", "mult.": 17, "alt_group": "*", "graph_path": "-4,-1,2"}, {"#seq_name": "contig_3", "length": 791086, "cov.": 155, "circ.": "N", "repeat": "N", "mult.": 15, "alt_group": "*", "graph_path": "-4,3"}, {"#seq_name": "contig_6", "length": 317090, "cov.": 147, "circ.": "N", "repeat": "N", "mult.": 16, "alt_group": "*", "graph_path": "4,6,1,4"}, {"#seq_name": "contig_5", "length": 220050, "cov.": 151, "circ.": "N", "repeat": "N", "mult.": 15, "alt_group": "*", "graph_path": "4,5"}, {"#seq_name": "contig_7", "length": 155068, "cov.": 311, "circ.": "Y", "repeat": "Y", "mult.": 28, "alt_group": "*", "graph_path": "7"}, {"#seq_name": "contig_4", "length": 10645, "cov.": 254, "circ.": "N", "repeat": "Y", "mult.": 18, "alt_group": "*", "graph_path": "4"}]}, {"name": "assembly_graph", "file_path": "tests/data/dummy/flye/assembly.gfa", "hid": "12345", "galaxy_id": null, "content": []}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/integronfinder2_output.json --- a/test-data/summarize/integronfinder2_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "1.6.1", "reference_database_version": "", "analysis_software_name": "integronfinder2", "results": [{"name": "integronfinder2_report", "file_path": "tests/data/dummy/integronfinder2/results.integrons", "hid": "12345", "galaxy_hid": "", "content": [{"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_42", "pos_beg": 41235, "pos_end": 41546, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_43", "pos_beg": 41543, "pos_end": 42391, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "attc_001", "pos_beg": 41600, "pos_end": 41701, "strand": -1, "evalue": 0.15, "type_elt": "attC", "annotation": "attC", "model": "attc_4", "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_44", "pos_beg": 42419, "pos_end": 43705, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_45", "pos_beg": 43702, "pos_end": 45213, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "attc_002", "pos_beg": 44054, "pos_end": 44100, "strand": -1, "evalue": 0.095, "type_elt": "attC", "annotation": "attC", "model": "attc_4", "type": "CALIN", "default": "No", "distance_2attC": 2353.0, "considered_topology": "lin"}]}, {"name": "summary", "file_path": "tests/data/dummy/integronfinder2/results.summary", "hid": "12345", "content": [{"ID_replicon": "contig00001", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 436224}, {"ID_replicon": "contig00002", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 252900}, {"ID_replicon": "contig00003", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 206370}, {"ID_replicon": "contig00004", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 168397}, {"ID_replicon": "contig00005", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 132811}, {"ID_replicon": "contig00006", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 115359}, {"ID_replicon": "contig00007", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 113419}, {"ID_replicon": "contig00008", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 99915}, {"ID_replicon": "contig00009", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 97190}, {"ID_replicon": "contig00010", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 92075}, {"ID_replicon": "contig00011", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 86662}, {"ID_replicon": "contig00012", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 82418}, {"ID_replicon": "contig00013", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 81741}, {"ID_replicon": "contig00014", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 81694}, {"ID_replicon": "contig00015", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 71911}, {"ID_replicon": "contig00016", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 66886}, {"ID_replicon": "contig00017", "CALIN": 1, "complete": 0, "In0": 0, "topology": "lin", "size": 645'..b'replicon": "contig00053", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1775}, {"ID_replicon": "contig00055", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1578}, {"ID_replicon": "contig00056", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1526}, {"ID_replicon": "contig00057", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1515}, {"ID_replicon": "contig00058", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1299}, {"ID_replicon": "contig00059", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 652}, {"ID_replicon": "contig00060", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 607}, {"ID_replicon": "contig00061", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 534}, {"ID_replicon": "contig00062", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 525}, {"ID_replicon": "contig00063", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 442}, {"ID_replicon": "contig00065", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 405}, {"ID_replicon": "contig00066", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 398}, {"ID_replicon": "contig00067", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 378}, {"ID_replicon": "contig00068", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 372}, {"ID_replicon": "contig00070", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 332}, {"ID_replicon": "contig00074", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 256}, {"ID_replicon": "contig00075", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00076", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00077", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00078", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00079", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00080", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00081", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00082", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00083", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00084", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00085", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00086", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 254}, {"ID_replicon": "contig00088", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 253}, {"ID_replicon": "contig00089", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 252}, {"ID_replicon": "contig00090", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 250}, {"ID_replicon": "contig00091", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 246}, {"ID_replicon": "contig00092", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 235}, {"ID_replicon": "contig00093", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 231}, {"ID_replicon": "contig00094", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 206}, {"ID_replicon": "contig00095", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 205}, {"ID_replicon": "contig00096", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 161}, {"ID_replicon": "contig00097", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 151}, {"ID_replicon": "contig00098", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 138}]}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/isescan_output.json --- a/test-data/summarize/isescan_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "1.7.2.3", "reference_database_version": "", "analysis_software_name": "isescan", "results": [{"name": "isescan_report", "file_path": "tests/data/dummy/isescan/results.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"contig00001": "contig00002", "IS21": "IS200/IS605", "IS21_259": "IS200/IS605_96", "104722": 179502, "106001": 180572, "1280": 1071, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 179502, "106043": 180572, "+": "-", "843": 1071, "2.1e-13": 1.2e-69, "2.1e-13.1": 1.2e-69, "p": "c", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00002", "IS21": "IS21", "IS21_259": "IS21_288", "104722": 210210, "106001": 214514, "1280": 4305, "1": 1, "104722.1": 210210, "104735": 210236, "105988": 214488, "106001.1": 214514, "20": 26, "12": 20, "14": 27, "0": 0, "105201": 210541, "106043": 214169, "+": "-", "843": 3629, "2.1e-13": 1e-10, "2.1e-13.1": 1e-10, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "ATTAAGCCAAATGGCAATGGTGATGAA:ATCAAGAAAAATGGGGATCGTGAAGAA"}, {"contig00001": "contig00002", "IS21": "IS30", "IS21_259": "IS30_241", "104722": 252678, "106001": 252900, "1280": 223, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 252678, "106043": 252900, "+": "+", "843": 223, "2.1e-13": 8.3e-32, "2.1e-13.1": 8.3e-32, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00005", "IS21": "IS30", "IS21_259": "IS30_241", "104722": 54, "106001": 3033, "1280": 2980, "1": 1, "104722.1": 54, "104735": 67, "105988": 3020, "106001.1": 3033, "20": 20, "12": 12, "14": 14, "0": 0, "105201": 1, "106043": 2892, "+": "+", "843": 2892, "2.1e-13": 6.2e-51, "2.1e-13.1": 6.2e-51, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "AAAAGAATTTTCTA:AAATGAATGTTCTA"}, {"contig00001": "contig00005", "IS21": "IS21", "IS21_259": "IS21_259", "104722": 84142, "106001": 85683, "1280": 1542, "1": 1, "104722.1": 84142, "104735": 84174, "105988": 85651, "106001.1": 85683, "20": 34, "12": 25, "14": 33, "0": 0, "105201": 84182, "106043": 85525, "+": "-", "843": 1344, "2.1e-13": 0.0, "2.1e-13.1": 0.0, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "TGTGGATAACTTTGTTCTTTTTTGTTTAGTTTT:TGTGGAAAACTTTTTTCACCCTTGTGTACTTTT"}, {"contig00001": "contig00008", "IS21": "IS30", "IS21_259": "IS30_241", "104722": 99798, "106001": 99915, "1280": 118, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 99798, "106043": 99915, "+": "-", "843": 118, "2.1e-13": 0.0, "2.1e-13.1": 0.0, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00010", "IS21": "IS6", "IS21_259": "IS6_292", "104722": 1, "106001": 138, "1280": 138, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 1, "106043": 138, "+": "-", "843": 138, "2.1e-13": 7.2e-22, "2.1e-13.1": 7.2e-22, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00010", "IS21": "IS256", "IS21_259": "IS256_47", "104722": 63216, "106001": 65257, "1280": 2042, "1": 1, "104722.1": 63216, "104735": 63259, "105988": 65215, "106001.1": 65257, "20": 26, "12": 30, "14": 44, "0": 1, "105201": 63507, "106043": 64842, "+": "-", "843": 1336, "2.1e-13": 4.3e-136, "2.1e-13.1": 4.3e-136, "p": "c", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "AGGGATTCTTAGAAGTAGAAGCTCAACATTTTGAACTTATAGAA:AGGCATTTGTGGAATTATACTTTCAATA-TTAGAACTTTTTGAA"}, {"contig00001": "contig00010", "IS21": "IS3", "IS21_259": "IS3_176", "104722": 65906, "106001": 67630, "1280": 1725, "1": 1, "104722.1": 65906, "104735": 65936, "105988": 67600, "106001.1": 67630, "20": 34, "12": 24, "14": 31, "0": 0, "105201": 65942, "106043": 67421, "+": "+", "843": 1480, "2.1e-13": 2.5e-113, "2.1e-13.1": 2.5e-113, "p": "c", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "TGGATAGGCTACAATTAACTAGACAGAAAAA:TGGATA'..b'ACTCTCTTCGGGTTTTCGGTCTGTACTGAAATCAAGGTATTATTGGGAATCCCAGCTTAAATCATAGATACCGTAAGGGATTTTATTCTTTATTTAAAACTTTGCAACAGAACC"}, "contig00076": {"sequence_informations": {"contig": "contig00076", "start": "1", "end": "223", "strand": "-", "family": "IS30", "cluster": "241"}, "sequence": "ATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAGAATCATATTATCTTCAACATAATAAACCGGTTGAAATCGCTAACCGAATGGGACGTGCTATACAAACTATTTATAATGTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATTGGCACCAGTATAAAGAAAATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC"}, "contig00079": {"sequence_informations": {"contig": "contig00079", "start": "1", "end": "255", "strand": "-", "family": "IS30", "cluster": "241"}, "sequence": "CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGGGATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACACCAATTG"}, "contig00083": {"sequence_informations": {"contig": "contig00083", "start": "135", "end": "255", "strand": "+", "family": "IS6", "cluster": "292"}, "sequence": "TTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAGG"}, "contig00085": {"sequence_informations": {"contig": "contig00085", "start": "1", "end": "255", "strand": "+", "family": "IS30", "cluster": "241"}, "sequence": "CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGGTATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACACCAATTG"}, "contig00090": {"sequence_informations": {"contig": "contig00090", "start": "1", "end": "250", "strand": "-", "family": "IS6", "cluster": "292"}, "sequence": "TGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAGGTTGTAGTCACAGATAAAGCCCCCCTCTATTACAAGTGCCTTTAAGAAACTAAAAGAATACGGCTTTTATCAAGGGACAGAACATCGTACCATTAAATACCTGAATAATTTGATTGAACAAGACCATCGTCCAGTAAAGAGACGCAA"}, "contig00093": {"sequence_informations": {"contig": "contig00093", "start": "1", "end": "231", "strand": "-", "family": "IS6", "cluster": "292"}, "sequence": "ATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAGGAAAATGGCATTATTTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAG"}, "contig00094": {"sequence_informations": {"contig": "contig00094", "start": "69", "end": "206", "strand": "+", "family": "IS6", "cluster": "292"}, "sequence": "ATGACGATGAGTCATTTTAAAGGAAAGCAATTTCAGCAGGATGTGATTATTGTAGCCGTGGGCTACTATCTTCGTTATAACCTTAGCTATCGTGAAGTTCAAGAAATCTTATATGATCGTGGCATTAACGTTTCTCAT"}, "contig00096": {"sequence_informations": {"contig": "contig00096", "start": "1", "end": "161", "strand": "-", "family": "IS30", "cluster": "241"}, "sequence": "TGGTTTTCTCGCTTCCCTAAAAACTTCTTTAAATCTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGG"}, "contig00097": {"sequence_informations": {"contig": "contig00097", "start": "1", "end": "151", "strand": "-", "family": "IS6", "cluster": "292"}, "sequence": "ATGATCGTGGCATTAACGTTTCTCATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAGGAAAATG"}, "contig00098": {"sequence_informations": {"contig": "contig00098", "start": "1", "end": "138", "strand": "+", "family": "IS30", "cluster": "241"}, "sequence": "ATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACACCAATTGAGATATTTTTG"}}}, {"name": "summary_path", "file_path": "tests/data/dummy/isescan/summary.tsv", "hid": "12345", "galaxy_id": "", "content": {}}, {"name": "annotation_path", "file_path": "tests/data/dummy/isescan/annotation.gff", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/kraken2_output.json --- a/test-data/summarize/kraken2_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_version": "2.1.2", "reference_database_version": "PlusPF_16", "analysis_software_name": "kraken2", "results": [{"name": "kraken2_report", "file_path": "tests/data/dummy/kraken2/taxonomy_report.tsv", "hid": "12345", "galaxy_id": null, "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": 4, "rank_code": "D", "ncbi_taxonomic_id": 2, "scientific_name": "Bacteria"}, {"fragment_coverage": 95.79, "fragment_number": 91, "assigned_fragment_number": 0, "rank_code": "D1", "ncbi_taxonomic_id": 1783272, "scientific_name": "Terrabacteria_group"}, {"fragment_coverage": 95.79, "fragment_number": 91, "assigned_fragment_number": 0, "rank_code": "P", "ncbi_taxonomic_id": 1239, "scientific_name": "Firmicutes"}, {"fragment_coverage": 95.79, "fragment_number": 91, "assigned_fragment_number": 4, "rank_code": "C", "ncbi_taxonomic_id": 91061, "scientific_name": "Bacilli"}, {"fragment_coverage": 89.47, "fragment_number": 85, "assigned_fragment_number": 8, "rank_code": "O", "ncbi_taxonomic_id": 186826, "scientific_name": "Lactobacillales"}, {"fragment_coverage": 78.95, "fragment_number": 75, "assigned_fragment_number": 0, "rank_code": "F", "ncbi_taxonomic_id": 81852, "scientific_name": "Enterococcaceae"}, {"fragment_coverage": 78.95, "fragment_number": 75, "assigned_fragment_number": 7, "rank_code": "G", "ncbi_taxonomic_id": 1350, "scientific_name": "Enterococcus"}, {"fragment_coverage": 66.32, "fragment_number": 63, "assigned_fragment_number": 42, "rank_code": "S", "ncbi_taxonomic_id": 1351, "scientific_name": "Enterococcus_faecalis"}]}, {"name": "seq_classification_file_path", "file_path": "tests/data/dummy/kraken2/taxonomy_result.tsv", "hid": "12345", "galaxy_id": null, "content": []}], "tool_has_database": true}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/multiqc_output.json --- a/test-data/summarize/multiqc_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_version": "1.11", "reference_database_version": "", "analysis_software_name": "multiqc", "results": [{"name": "multiqc_report", "file_path": "tests/data/dummy/multiqc/multiqc_report.html", "hid": "12345", "galaxy_hid": "", "content": {}}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/polypolish_output.json --- a/test-data/summarize/polypolish_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "0.5.0", "reference_database_version": null, "analysis_software_name": "polypolish", "results": [{"name": "polypolish_report", "file_path": "tests/data/dummy/polypolish/polished_assembly.fasta", "hid": "12345", "galaxy_id": null, "content": [{"name": "contig_6_polypolish", "length": 320811, "sequence": "ATAACCCGGATATTTTTGATCTTACCGAAGCGCAGCAACTGACTGCTGAAGAGCAGGTCGAAAAATGGGTGGATGGCAGGAAAAAAATACTGTGGGACAGCAAAAAGCGACGCAATGAGGCGCTCGACTGCTTCGTTTATGCGCTGGCGGCGCTGCGCATCAGTATTTCCCGCTGGCAGCTGGATCTCAGTGCACTGCTGGCGAGCCTGCAGGAAGAGGATGGTGCAGCAACCAACAAGAAAACACTGGCAGAATACGCCCGTGCCTTATCCGGAGAGGATGAATGACGCGACAGGAAGAACTTGCCGCTGCCCGTGCGGCACTGCATGACCTGATGACAGGAAAACGGGTGGCAACGGTACAGAAAGACGGACGGCGAGTGGAGTTTACGACCACTTCCGTGTCTGACCTGAAAAATACATTGCTGAGCTGGAAGTGCAGACCGGCATGACACAGCGACGCAGGGGACCAGCAGGATTTTATGTATGAAAATGTCCACCATTCCCACCCTTCTGGGGCCGGACGGCATGACATCGCTGCGTGAATATGCCGGTTATCACGGCGGTGGCAGCGGATTTGGTGGGCAGTTGCGGGCGTGGAACCCACCGGGTGAAAGTGTGGATGCAGCCCTGCTGCCCAACTTTACCCGTGGCAATGCCCGCGCAGACGATCTGGTACGCAATAACGGCTATGCCGCCAACGCCATCCAGTTGCATCAGGATCATATCGTCGGGTCTTTTTTCCGGCTCAGTCATCGCCCAAGCTGGCGCTATCTGGGCATCGGGGAGGAAGAAGCCCGTGCCTTTTCCCGCGAGGTTGAAGCGGCATGGAAAGAGTTTGCCGAAGATGACTGTTGCTGCATTGACGTTGAGCGAAAACGCACGTTTACCATGATGATTCGGGAAGGTGTGGCCATGCACGCCTTTAACGGTGAACTGTTCGTTCAGGCCACCTGGGATACCCGTCCCTCGCGACTGTTCCGGACACAGTTCCGGATGGTCAGCCCGAAGCGCATCAGCAACCCGAACAATACCGGCGACAGCCGGAACTGCCGTGCCGGTGTGCAGATTAATGACAGCGGTGCGGCGCTGGGATATTACGTCAGCGAGGACGGGTATCCTGGCTGGATGCCGCAGAAATGGACATGGATACCCCGTGAGTTACCCGGCGGCGCGCCTCGTTCATTCACGTTTTGAACCCGTGGAGGACGGGCAGACCCGCGGTGCAAATGTGTTTTACAGCGTGATGGAGCAGATGAAGATGCTCGACACGCTGCAGAACACGCAGCTGCAGAGCGCCATTGTGAAGGCGATGTATGCCGCCACCATTGAAAGTGAGCTGGATACGCAGTCAGCGATGGATTTTATTCTGGGCGCGAACAGTCAGGAGCAGCGGGAAAGGCTGACGGGCTGGATTGGTGAAATTGCCGCGTATTACGCCGCAGCACCGGTCCGTCTGGGAGGCGCAAAAGTGCCGCACCTGATGCCGGGGACTCACTGAACCTGCAGACGGCTCAGGACACGGATAACGGCTACTCCGTGTTTGAGCAGTCACTGCTGCGGTATATCGCTGCCGGGCTGGGTGTCTCGTATGAGCAGCTTTCCGGAATTACGCCCAGATGAGCTACTCCACGGCACGGGCCAGTGCGAACGAGTCGTGGGCGTACTTTATGGGGCGGCGAAAATTCGTCGCATCCCGTCAGGCGAGCCAGATGTTTCTGTGCTGGCTGGAAGAGGCCATCGTTCGCCGCGTGGTGACGTTACCTTCAAAAGCGCGCTTCAGCTTTCAGGAAGCCCGCAGTGCTGGGGGAACTGCGACTGGATAGGCTCCGGTCGTATGGCCATCGATGGTCTGAAAGAAGTTCAGGAAGCGGTGATGCTGATAGAAGCCGGACTGAGCACCTACGAGAAAGAGTGCGCGAAACGCGGTGACGACTATCAGGAAATTTTTGCCCAGCAGGTCCGTGAAACGATGGAGCGCCGCGCAGCTGGTCTTAAACCGCCCGCCTGGGCGGCTGCGGCATTTGAATCCGGGCTGCGACAATCAACAGAGGAGGAGAAGAGTGACAGCAGAGCTGCGTAATCTCCCGCATATTGCCAGCATGGCTTTTAATGAGCCGCTGATGCTTGAACCCGCCTATGCGCGGGTTTCTTTGTGCGCTTGCAGGCCAGCTTGGGATCAGCCGCCTGACGGATGCAGTATCCGGCGACAGCCTGACTGCCGGAGAGGCACCCGCGGCGCTGGCGTTATCCGGTGATGATGACGGACCACGACAGGCCCGGAGTTATCAGGTCATGAACGGCATCGCCGTGCTGCCGGTGTCCGGTACGCTGGTCAGCCGGACGCGGGCGCTGCAGCCGTATTCGGGAATGACCGGTTACAACGGCATTATCGCCCGTCTGCAACAGGCTGCCAGCGATCCGATGGTGGACGGCATTCTGCTCGATATGGACACACCGGGCGGGATGGTGGCGGGAGCATTTGACTGTGCTGACATCATCGCCCGTGTGCGAGACATAAAACCGGTATGGGCGCTGGCCAACGACATGAACTGCAGTGCAGGTCAGCTGCTTGCCAGCGCCGCCTCCCGGCGTCTGGTCACGCAGACCGCCCGGACAGGCTCCATCGGCGTCATGATGGCTCACAGTAATTACGGTGCTGCCTGGAGAAACAGGGCGTGGAAATCACGCTGATTTACAGCGGCAGCCATAAGGTGGATGGCAACCCTACAGCCATCTACCGGGTGATGTCCGGGAAACACTGCAGTCCCGGATGGATGCAACCCGCCGGATGTTTGCGCAGAAGGTGTCGGCATATACCGGCCTGTCCGTGCAGGCTGTGCTGGATACCGAGGCTGCAGTGTACAGCGGTCAGGAGGCCATTGATGCCGGACTGGCTGATGAACTTGTCAACAGCACCGATGCGATCACCGTTATGCGTGATGCACTGGATGCACGTAAATCCCGTCTCTCAGGAGGGCGAATGACCAAAGAGACTCAATCAACAACTGTTTCAGCCACTGCTTCGCAGGCTGACGTTACTGGCGTGGTGCCAGCGACGGAGGGCGAAAACGCCAGCGCGGCGCAGCCGGACGTGAACGCGCAGATCACCGCTGCGGTTGCGGCAGAAAACAGCCGCATTATGGGGATCCTCAACTGTGAGGAGGCTCACGGACGCGAAGAACAGGCCCGCGTGCTGGCAGAAACCCCGGTATGACCGTGGAAACGGCCCGCCGCATTCTGGCCGCAGCACCACAGAGTGCACAGGCGCGCAGTGATACTGCGCTGGATCGTCTGATGCAGGGGCACCGGCACCGCTGGCTGCAGGTAACCCGGCATCTGATGCCGTTAACGATTTGCTGAACACACCAGTGTAAGGGATGTTTATGACGAGCAAAGAAACCTTTACCCATTACCAGCCGCTGGGCAACAGTGACCCGGCTCATACCGCAACCGCGCCCGGCGGATTGAGTGCGAAAGCGTCTGCAATGACCCCGCTGATGCTGGACACCGCCACCCGTAAGCTGGTTGCGTGGGATGGCACCACCGACGGTGCTGCCGTTGGCATTCTTGCGGTTGCTGCTGACCAGACCAGCACCACGCTGACGTTCTACAAGTCCGGCACGTTCCGTTATGAGGATGTGCTC'..b'TTCCTGTAGGCTAATCACTGTGTCTGGGTAAACAACAGATATCTGGTGGCGATATGCAGGAACGTATTGATTATCATATTGAGAAATATCAGTTCAGGGCGAGGAATGAGTCTCCACGACTGATGCGTCAGTGGGCTTATGTCATGCGTGAATGCCGGGAGACCAGGGCTGGAGCCAGGGAGCGACTGCGGACAGCATTACTGAATGTTGATTATGTGACCAGTTTTGAGCTGCCGTTTCGTCTGCTGTTAACCCGGACACCGCAGATGATTGACACTCTGCGTCGGGAATGCCTGCTCAGCCAGAAAAAAGCCCTGTTCAACGGGCGGCAGCGGGGATGTGTATACAGTCTGCAGAATGACTTATCCGGTGTGCCGGATTGTTTCAGCTACAGTCTTGCGACGCGAATACGGCGGATGGACTGCTATGGCATGACGACGCGTTGTTTTACTGATATCGCCGGGCAGGTTAAAGCCCCGACGGCACGGCTGAAACTGGCGCTGGAAAGCGGGTTGCTGGTAACGGCACTGGATGGCCTGTTCTGGCTGGGAACTCAGCGAATTGCAGCTGATGTGCAGAGACTGCGTCAGTCAGGTATGGTTATAGTCACCCGGGAAGTTGAGGTATCAGACTCCCTGACCGGAACCACCAGACTGGTTTCTGCTTACACACTTTAAAGCACAGGAGGAATCTTTGTTACCGTATTCGCACTGATTCTGAAATTTACCATTGTTTACCGGGACAGATTACAGACAGGATATTTTATGCGAGATAAATCGAAGTATTAACCGAGCGCAGAAAACAGATTTGGTCTGATTCTTTATATTATACTATTATCAGTTATTTATATATTGATAACAAGACTTAATCTCACAACCACATATTATTCGCTGTATTCATCTCTGGATGAGAATTCACAGGTGACGGAGTATTTTATAATATCCATAGCCACCTTTCTTTTCTGGCGGCTTTATGTTTGTTCTTCATTTATTCTTTCTTTAAACGGAAAAGAGTTGTCGGGAAATTACTTCTGTGCATTTATATTCTTATATATCACACTATGCTATCACTTTTGTTTATTGTCTTTATGTTGTCGGTGCTGAGTGTATGGCAACCGGAGGTAGTGCATCCAATTAGTAGAACATGTGTTTTTCGATAAACGCTCCGATCACTTTTTCGTGGATCTCAACTGAGCGTGAGAAGCAGATTGTTTTACGAGCCAACCGCTTAATGCGGGTGCGTAGCGTCAGATTATTACGCTCAATGCGTTGGGTGAATATTTTGCCGGTCAGATGCTTATTCTTCGGCACCTCCCGGCCATAGCTGCCCCAGTCATCGCTGGTCAGCATGCCGATGTTGAAGGTGTAAGCAGTGCCAGTAGCTCCCGGCACGTTTGATCGGTTCGGGGACCAAAGTGTAGGCCAGTACACCGCCTGTTTTGGTGTTGTACGCGTACCAGAGCCAGTGTTGCCGGGCTTTACTGCCAACGTAGCTCCATTGCTCATCAAGCTCGCAGATAAGCGCCACATCAGCATGGGCAACAGGCGAAGACGTTATTCGCTTTGGCGCGAGTTTTTAAAGTCCGGATGACGGTGTTAATACCAATTTTCAGTGTCCTGGCGGTATCGCGAACCCCGGCACCATTAAAGGCCATTTCAGTTATCAGCTCTTTCATACCCGGCTTACGTGCTTGATAAGTATAAGTGAGCTGAAACACACGGTGGCAGTCACGGCAGCGAAATCTGTCACGGCCTTTAGGGTTCTGACCATGGCGGTAAACCTGAGCTGACTGACAACGGGGACAATGAATATTAACGCTGGCCATGAGATAACCTCAAAAGCCCGTATTATACATCAGATTCAACTAATTAGAGGCATCACCCATGAGCAATTGTTTTTGCAGTGCTCAATGATATTAAATTATTGATGATACTATTGTGTTCTTGGCGAGAATCTTGTTGAAGTAATTGCTGAGATCATTCACAGTGTTTATATCGTTGAACTCAAGAAACTCAGAAGGAAGCAGGCGTTTGATTGCTCCACGTATTCCCCCGGACGATCGTTGATGTGTTTGAGTAAGTTTTTTTAGCGAGACGCCCTCCGCTATGGATACGAGAAGACGCTGTAACTCTTCAGTATTCCATGGAGTACCATGTCGTGCTGGAAAATTGCTGCGGATTCAGACATGATTTTATCTTTATGTTTTCTAGGTACTGCCTTGAGTGTGTGGATATGATAATTATTTATAATGATATTGTTATCTTTATAGATAACTGATATGCAGAATTGTATTGATTTTGTCTACAGTGGGCAAGACAGTGCTAAGAATTTGTGGGGAAAAATAGAGACTCCATGCGGCGTCCTGAGATAGACGGCAGACAGGCATTCTGCCTGAAAAGAAAAAGCCGGTTCAGAGAAAACCGGCTGACGGATTACCGTCTAACAGTTGGTCGCTACCTTAAAATACTTCTGCAACAGGCACACCGGCAACTTTTTCCCACTCTTTAACCCGATACCGGATCATCTGCGGGAAACGTTCCTTGTACTCATATCCACGTGCAGCCATGGTGTGCATGGTGTTGGCCAGTGTCCTTGATGAGATGCCGGAGATTTCAAGAGGGATCATCGGCAGACTCACATAGGTGGTGTGGATTTCCAGCTTGCCGTCTTCAGCAACTGTTCGGGTGAAGTTGTGAATATCCAGACCAATCACATCCATGACATTGTTTGGGTAAATGCGCACATACAGCATGGTGCCGTTTTTAATGTCGATCCCGAAATAACAACTCTTCGAGAATGACAGTTGCTCGTAATCGCTAGTCGGCGCAAAGGGACTGCTTTCTTTTATCTTCTTAACAACCTGTAGGATTTTCTTTGCCTTAGTTCTCAGATATAGCCATAGTGAAGGAATTATTAATAGAAACCAACTGCCACAAGTATATAGATATGCTTGAATATCTGTTCCTATATATGGTTCTGTAAGCATCATGCCGGTAAAGCCTAGAGAACATAACAATAAAAAAGGAATGCCAAATATAAAGTAAGTGTTGCGAATAAGATAATAATATCCCCACCAGGAAGGATATCTGTTTTTTGTTGTATTCATAATGAACCCCCATATTCACCTGAATGTATTTTAATCTCTTCAGGTGAATATGGCAATACTGTTTTGTACTCTATTGTTTTATTCCGTCCTTATCATCTCCATTAATATTTTTCAGTTTTTCTTCACGAACGCCAGGTGTTCTGCGTATATTGGTGTTTCCGCCGGCAATAATATCTTTGACGGAAGAAACCATATTTCCCAGCATATTAACGCCGTCACGTCCACCCAGAAAATTAATCACATGGTCTGGCAGATAAGCCTGAAGTGCAAAAACGCCCGCAACCAGTGTGGTACAGGCGCGGGCATAAATCATCAAAAATCCCGCCATGCTGAACACCCCCGTCACAGAATTTATCTGGACATTCATTAGTGCTGCAGCGTACAGAGCATTCAGTATGGTGCCGCCAGCCACGATGGCGACCGATGCAAAAAAGAACCCGAACACCATCAGCAGTGGCCTGATCATGCTGTCTATCAGGTAGATGTAACCGTAAGCGGCCCGACTTCCTCTGTCCTGACTTGTTCCCAGGTGGGTTGCGGCCCACAGGGGGCCGGCGGCGCATCCAATCAGTACACTGACTATCCAGTTACCGATGCCGGTCATCCAGAAGATAAACGGAATAAACGGCAGGTAAATGGATAACGAAAAACCGGCACAGAACAGCAAAAACAGCAGGAAGTAGAGCGGTGGTGCAGCTGCTTCCAGAAAAGCCTTTGCGGCATCAGATAAGCCGCTAACAGCATTGACCAGTCGACCAAAATGGAGTTGCTGCCGGCAGTGGAAAGCACCTGACGGTGGTATAACCCGCCCAGATGGTTTCGGTTGTGA"}]}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/quast_output.json --- a/test-data/summarize/quast_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"reference_database_version": "", "analysis_software_version": "5.0.2", "analysis_software_name": "quast", "results": [{"name": "quast_report", "file_path": "tests/data/dummy/quast/quast_result.tsv", "hid": "12345", "galaxy_hid": "", "content": {"Assembly": "10_Enterococcus_faecalis_S17_L001", "contigs_(>=_0_bp)": "100", "contigs_(>=_1000_bp)": "58", "contigs_(>=_5000_bp)": "48", "contigs_(>=_10000_bp)": "41", "contigs_(>=_25000_bp)": "28", "contigs_(>=_50000_bp)": "20", "Total_length_(>=_0_bp)": "3027634", "Total_length_(>=_1000_bp)": "3015201", "Total_length_(>=_5000_bp)": "2996428", "Total_length_(>=_10000_bp)": "2944723", "Total_length_(>=_25000_bp)": "2735277", "Total_length_(>=_50000_bp)": "2421445", "contigs": "62", "Largest_contig": "436224", "Total_length": "3017519", "GC_(%)": "37.31", "N50": "99915", "N90": "27780", "auN": "154096.4", "L50": "8", "L90": "28", "total_reads": "3489582", "left": "1744791", "right": "1744791", "Mapped_(%)": "99.85", "Properly_paired_(%)": "98.83", "Avg._coverage_depth": "230", "Coverage_>=_1x_(%)": "100.0", "N's_per_100_kbp": "0.00"}}, {"name": "quast_html_path", "file_path": "tests/data/dummy/quast/quast_report.html", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/recentrifuge_output.json --- a/test-data/summarize/recentrifuge_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "5.0.2", "reference_database_version": "1.9", "analysis_software_name": "recentrifuge", "results": [{"name": "recentrifuge_report", "file_path": "tests/data/dummy/recentrifuge/rcf_data.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"Stats": "Id", "count": null, "unassigned": null, "score": null, "Rank": null, "Name": null}, {"Stats": "1", "count": 1705098.0, "unassigned": 8766.0, "score": 23.4065769383, "Rank": "no_rank", "Name": "root"}, {"Stats": "2", "count": 1696077.0, "unassigned": 41771.0, "score": 23.3954250828, "Rank": "superkingdom", "Name": "Bacteria"}, {"Stats": "1224", "count": 656.0, "unassigned": 8.0, "score": 2.5291006276, "Rank": "phylum", "Name": "Proteobacteria"}, {"Stats": "1236", "count": 626.0, "unassigned": 12.0, "score": 2.4820475721, "Rank": "class", "Name": "Gammaproteobacteria"}, {"Stats": "91347", "count": 614.0, "unassigned": 1.0, "score": 2.4579418683, "Rank": "order", "Name": "Enterobacterales"}, {"Stats": "543", "count": 613.0, "unassigned": 320.0, "score": 2.4604241069, "Rank": "family", "Name": "Enterobacteriaceae"}, {"Stats": "2890311", "count": 293.0, "unassigned": 0.0, "score": 3.2460969909, "Rank": "no_rank", "Name": "Klebsiella/Raoultellagroup"}, {"Stats": "570", "count": 293.0, "unassigned": 0.0, "score": 3.2460969909, "Rank": "genus", "Name": "Klebsiella"}, {"Stats": "573", "count": 37.0, "unassigned": 37.0, "score": 0.8707595857, "Rank": "species", "Name": "Klebsiellapneumoniae"}, {"Stats": "1463165", "count": 256.0, "unassigned": 256.0, "score": 3.5894074753, "Rank": "species", "Name": "Klebsiellaquasipneumoniae"}, {"Stats": "28211", "count": 14.0, "unassigned": 3.0, "score": 3.5108263106, "Rank": "class", "Name": "Alphaproteobacteria"}, {"Stats": "204455", "count": 11.0, "unassigned": 0.0, "score": 3.9118522954, "Rank": "order", "Name": "Rhodobacterales"}, {"Stats": "31989", "count": 11.0, "unassigned": 5.0, "score": 3.9118522954, "Rank": "family", "Name": "Rhodobacteraceae"}, {"Stats": "2083206", "count": 6.0, "unassigned": 0.0, "score": 5.0030001348, "Rank": "genus", "Name": "Tritonibacter"}, {"Stats": "379347", "count": 6.0, "unassigned": 6.0, "score": 5.0030001348, "Rank": "species", "Name": "Tritonibactermobilis"}, {"Stats": "68525", "count": 8.0, "unassigned": 2.0, "score": 6.4392025411, "Rank": "subphylum", "Name": "delta/epsilonsubdivisions"}, {"Stats": "29547", "count": 6.0, "unassigned": 0.0, "score": 6.4917947578, "Rank": "class", "Name": "Epsilonproteobacteria"}, {"Stats": "213849", "count": 6.0, "unassigned": 6.0, "score": 6.4917947578, "Rank": "order", "Name": "Campylobacterales"}, {"Stats": "203691", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "phylum", "Name": "Spirochaetes"}, {"Stats": "203692", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "class", "Name": "Spirochaetia"}, {"Stats": "1643686", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "order", "Name": "Brachyspirales"}, {"Stats": "143786", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "family", "Name": "Brachyspiraceae"}, {"Stats": "29521", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "genus", "Name": "Brachyspira"}, {"Stats": "52584", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "species", "Name": "Brachyspirapilosicoli"}, {"Stats": "759914", "count": 8.0, "unassigned": 8.0, "score": 2.6705569199, "Rank": "strain", "Name": "Brachyspirapilosicoli95/1000"}, {"Stats": "1783257", "count": 9.0, "unassigned": 1.0, "score": 5.6663185939, "Rank": "no_rank", "Name": "PVCgroup"}, {"Stats": "204428", "count": 8.0, "unassigned": 0.0, "score": 6.1710253563, "Rank": "phylum", "Name": "Chlamydiae"}, {"Stats": "204429", "count": 8.0, "unassigned": 0.0, "score": 6.1710253563, "Rank": "class", "Name": "Chlamydiia"}, {"Stats": "1963360", "count": 8.0, "unassigned": 0.0, "score": 6.1710253563, "Rank": "order", "Name": "Parachlamydiales"}, {"Stats": "92713", "count": 8'..b'assigned": 0.0, "score": 4.2516471932, "Rank": "suborder", "Name": "Haplorrhini"}, {"Stats": "314293", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "infraorder", "Name": "Simiiformes"}, {"Stats": "9526", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "parvorder", "Name": "Catarrhini"}, {"Stats": "314295", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "superfamily", "Name": "Hominoidea"}, {"Stats": "9604", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "family", "Name": "Hominidae"}, {"Stats": "207598", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "subfamily", "Name": "Homininae"}, {"Stats": "9605", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "genus", "Name": "Homo"}, {"Stats": "9606", "count": 133.0, "unassigned": 133.0, "score": 4.2516471932, "Rank": "species", "Name": "Homosapiens"}, {"Stats": "10239", "count": 66.0, "unassigned": 0.0, "score": 4.7615627065, "Rank": "superkingdom", "Name": "Viruses"}, {"Stats": "2731341", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "no_rank", "Name": "Duplodnaviria"}, {"Stats": "2731360", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "kingdom", "Name": "Heunggongvirae"}, {"Stats": "2731618", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "phylum", "Name": "Uroviricota"}, {"Stats": "2731619", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "class", "Name": "Caudoviricetes"}, {"Stats": "10699", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "family", "Name": "Siphoviridae"}, {"Stats": "196894", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "no_rank", "Name": "unclassifiedSiphoviridae"}, {"Stats": "1747326", "count": 41.0, "unassigned": 41.0, "score": 4.7752963479, "Rank": "species", "Name": "EnterococcusphagevB_EfaS_IME197"}, {"Stats": "2732004", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "no_rank", "Name": "Varidnaviria"}, {"Stats": "2732005", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "kingdom", "Name": "Bamfordvirae"}, {"Stats": "2732007", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "phylum", "Name": "Nucleocytoviricota"}, {"Stats": "2732523", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "class", "Name": "Megaviricetes"}, {"Stats": "2732554", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "order", "Name": "Imitervirales"}, {"Stats": "549779", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "family", "Name": "Mimiviridae"}, {"Stats": "985780", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "no_rank", "Name": "unclassifiedMimiviridae"}, {"Stats": "985782", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "species", "Name": "Moumouvirus"}, {"Stats": "1269028", "count": 25.0, "unassigned": 25.0, "score": 4.7390395347, "Rank": "no_rank", "Name": "Acanthamoebapolyphagamoumouvirus"}]}, {"name": "recentrifuge_statistics", "file_path": "tests/data/dummy/recentrifuge/rcf_stat.tsv", "hid": "12345", "content": [{"infos": "Seqs.read", "value": 1720128.0}, {"infos": "Seqs.unclass", "value": 15028.0}, {"infos": "Seqs.class", "value": 1705100.0}, {"infos": "Seqs.filtered", "value": 1705100.0}, {"infos": "Scoremin", "value": 35.0}, {"infos": "Scoremean", "value": 111.2545152777}, {"infos": "Scoremax", "value": 295.0}, {"infos": "Lengthmin", "value": 70.0}, {"infos": "Lengthmean", "value": 403.0}, {"infos": "Lengthmax", "value": 602.0}, {"infos": "Totalntread", "value": 690189277.0}, {"infos": "TIDsclass", "value": 426.0}, {"infos": "TIDsfiltered", "value": 425.0}, {"infos": "TIDsfolded", "value": 166.0}, {"infos": "Scorelimit", "value": null}]}, {"name": "recentrifuge_report", "file_path": "tests/data/dummy/recentrifuge/rcf_report.html", "hid": "12345", "content": ""}], "tool_has_database": true}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/refseqmasher_output.json --- a/test-data/summarize/refseqmasher_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"reference_database_version": "", "analysis_software_version": "1.0", "analysis_software_name": "refseqmasher", "results": [{"name": "refseqmasher_report", "file_path": "tests/data/dummy/refseqmasher/refsesqmasher.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis EnGen0295", "distance": 0.00802142, "pvalue": 0.0, "matching": "314/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0295", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN00809230", "taxid": 1158669, "assembly_accession": "GCF_000395135.1", "match_id": "./rcn/refseq-NZ-1158669-PRJNA224116-SAMN00809230-GCF_000395135.1-.-Enterococcus_faecalis_EnGen0295.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis EnGen0425", "distance": 0.00869982, "pvalue": 0.0, "matching": "308/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0425", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02333901", "taxid": 1391495, "assembly_accession": "GCF_000519925.1", "match_id": "./rcn/refseq-NZ-1391495-PRJNA224116-SAMN02333901-GCF_000519925.1-.-Enterococcus_faecalis_EnGen0425.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis ATCC 4200", "distance": 0.00916272, "pvalue": 0.0, "matching": "304/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; ATCC 4200", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02595252", "taxid": 565642, "assembly_accession": "GCF_000157195.1", "match_id": "./rcn/refseq-NZ-565642-PRJNA224116-SAMN02595252-GCF_000157195.1-.-Enterococcus_faecalis_ATCC_4200.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis ATCC 29212", "distance": 0.00975375, "pvalue": 0.0, "matching": "299/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; ATCC 29212", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02870637", "taxid": 1201292, "assembly_accession": "GCF_000742975.1", "match_id": "./rcn/refseq-NZ-1201292-PRJNA224116-SAMN02870637-GCF_000742975.1-.-Enterococcus_faecalis_ATCC_29212.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis EnGen0417", "distance": 0.0101152, "pvalue": 0.0, "matching": "296/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0417", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02333893", "taxid": 1391487, "assembly_accession": "GCF_000519765.1", "match_id": "./rcn/refseq-NZ-1391487-PRJNA224116-SAMN02333893-GCF_000519765.1-.-Enterococcus_faecalis_EnGen0417.fna"}]}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/shovill_output.json --- a/test-data/summarize/shovill_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "1.1.0", "reference_database_version": "", "analysis_software_name": "shovill", "results": [{"name": "shovill_report", "file_path": "tests/data/dummy/shovill/contigs.fa", "hid": "12345", "galaxy_hid": "", "content": {"contig00001": {"length": 436224, "coverage": 31.3, "sequence": "CTTTCTATCTTAGATTTTTGGTCGTACTTAAATTTTACTAGATAGACGACATGTTTTATATTTAAATAAACTAAAAAAGGACTGATGAATCAAAATTTGATTCATCAGTCCTTTAAATTATAGAGCCGTTAAAGACAGCCACAGCACGTGGCTGTCTTTTTTATTTTTTGTTATTTTTTCATTCTATTAAAATACCTGAGAAGTTTTCTTTTTTCTTAAGCTTGATTATGATAGAATGATTGGGTAGTTTATTTAGAAAACGTATATTACAGATAGGTGAGAATATAAATGAAAAAAATCGTAATCAATGGGAATCGTCCATTAAAGGGCGAAGTAACCATTAGCGGCGCCAAAAATAGTGTGGTCGCTTTAATTCCAGCTGCTATTTTAGCAGATTCGCCCGTGACTTTAGATGGCGTTCCTGACATTCAGGATGTTCACTCATTAATTGAAATATTAGAAATTATGGGTGCTAAAATTACTTTTGAAAATAATACATTAATTATTGACCCAACAGAAGTTGTTTCTGTGCCTATGCCAAAAGGAAAAATCAATAGCTTACGTGCATCCTATTATTTTATGGGCTCACTTCTTGGTCGATTTGGGGAAGGCGTTGTCGGCTTACCTGGCGGTTGTTACTTAGGACCTCGTCCAATTGATTTACATATCAAAGGATTTGAAGCATTAGGCGCTCATGTAACCAACGAACATGGGGCGATGTACTTGAGAACAGACGAAGCTGGCTTACAAGGAACACGAATTTTTATGGATATGGTATCTATTGGCGCTACAATCAATGTCATGTTAGCCGCAGTTAAAGCCAAAGGCAAAACGATTATTGAAAATGCTGCGCGTGAGCCAGAAATCATTGATATTGCTACATTATTAAATAACATGGGTGCAAAAGTTCGAGGAGCTGGAACGGACGTTATTCGGATTGAAGGTGTCGAAGAATTACATGGCTGTCGTCACTCGATTATTCCAGATCGAATTGAAGCTGGGACTTATTTAGCTATGGCAGCAGCTATGGGTGAAGGAATCAAGGTTCGAAATGTTATTTATGAGCATTTAGAAAGCTTCATTGCGAAATTGCAAGAAATGGGCGTTAAGATGACAATTGAAGAAGACATGATTGAAGTTCATCCGTCACATGATCTGAAAATGACGACGGTGAAAACCTATCCGTATCCTGGTTTTGCCACAGACTTGCAACAACCGTTAACGCCATTACTTTTAAAAGCACAAGGAACTGGTGAAATTATTGATACGATTTATGCTCAACGAAATAAGCATATCCCTGAGTTGGTGCGGATGGGGGCTGATGCTTCGGTTGAAGGCAATATGATTATCTTAAATGGCCCAAATCAATTGCACGGTGCAGAAGTAGTCGCCTCTGATTTACGGGCAGGCGCTTGCCTAGTCACTGCCGGCTTGATGGCTGAAGGTACGACCACTATTTATAATGTAGAATATATTTTACGTGGGTACGACCACATTATCGAAAAGTTAACTGCTTTAGGCGCTGATATTCAAATGCTAGAAACCGAAGAACAAGAAGGTCCGTTTGAGGTGGATCAATGAGCGACTATTTAACAATGGCTGAATTGGAAAACAGTACGTTAAAAGATATTTATGCATACGCGAAAGAGTTTAAAATTCCTTATTATAGCCAAATGAACAAAAAAGAATTGTCTTTAGCTGTGATTCGTGCACAAGCTGAGAAGCAAGGGTTTTTCTTCATGGAAGGAATTTTAGATATTGTTTCTCAGGATGGTTATGGTTTTTTGCGACCAATTAATTATGGACCAAGTGCAGAAGACATTTATATTTCTTCTTCTCAAATTCGTCGTTTCGGATTGAGAAATGGGGACAAAGTAGCTGGCAAGGCGCGTCCGCCAAAGGAATCAGAACGTTACTATGGACTCATGCATGTTGAAAGTGTCAATGGGAAAGATCCTGAAGAAGCGAAAGAGCGGCCACATTTTCCAGCGCTAACACCGTTGTATCCTGAAAAACAATTAACGTTAGAAACAACGGCTGGCAGATTATCAACACGAATGATTGATGTATTTGCCCCAATTGGTTTTGGGCAACGTGGTTTAATTGTAGCGCCGCCAAAAGCGGGGAAAACAAGTGTTTTAAAGGAAATTGCTAATGGGATTACAGAAAATCATCCTGATGTGGAATTGATTCTGTTGTTAATTGACGAGCGTCCTGAAGAAGTGACTGATTTAGAGCGAAGTGTTAAAGGCGATGTGGTTTCTTCAACTTTTGATCAACAACCACAAAATCATACGCGAGTTGCTGAATTGGTTCTGGATCGAGCAATGCGCTTAGTTGAAGACAAACGGGACGTAGTTATTTTAATGGACAGCATCACTCGTTTAGCAAGGGCCTATAATTTAGTGGTCCCGCCTAGTGGTCGAACCTTAAGTGGTGGAATAGATCCAGCTGCGTTTTTCAAACCTAAACGATTTTTTGGTGCTGCCAGAAATATCGAAGAAGGGGGCAGTCTGACTATTTTAGCCACGGCATTGGTGGATACAGGTAGCCGAATGGATGATGTCATCTATGAAGAATTCAAAGGCACAGGCAACATGGAGCTCCATTTATCTCGTGAATTAGCAGAGCGCCGTATTTTCCCAGCAATTGATATTAAAAAATCAAGTACGCGAAAAGAAGAGTTGCTAATGACACCAGAACAACTAGAAGAAACGTGGAAATTGAGAAATAATATGTCAGGAGACTCGCTGGAATATACGGATCAATTCATAAAAATGTTGAAACGGACCCAAAATAATCAACAATTATTTGAAGTTTTCCATGATGTTTCGTTTGGCAAACAAATTAAAAGAAATCCAAAAAGATAATTGCATACCAACTGAAAACATGGTAAGATAGCATTGTTGTATACCGACAAAATAACTCTGATACAGCAAATGGATCAGGGCAAAGGAGCGAAAAAACGTATGAAACAAGATATCCATCCAAATTACCAACCAGTAGTATTCATGGATTCAACAACAGGTTTCAAATTCCTTTCAGGTTCAACTAAAGGATCTTCAGAAACTGTTGAATGGGAAGATGGCAACACTTATCCATTATTACGTGTTGAGGTTACTTCAGACTCACACCCATTCTACACTGGTCGTCAAAAATTCACACAAGCCGACGGACGTGTGGACCGTTTCAACAAAAAATACGGTCTCAAAGACGAAAACGCAAATCCAGACGCATAGTCTTTCAAAACATTGTTATGACAAGGTTTATAGAGGTTTTCCACTGTGGTGGGAAACCTCTTTTTTGCGTTAAATATGTAGTTTTAATTCAGAGAAAAGAAATAAAGCAACTTACCAATCTTTTCCTCTTTCTTTTCAAGATTATCCTTCCCAAAAGTCAAAGATTGATCAGCATTGTTTCGCTGATTTGTTAGACTAGTAGGTACATTCAGCTTTATAAAGGAGATCTTGAAGAAATGAGTAGAAAAAAAGTCGGTGTTTTCTGTCTATTTCTGTTTTTCACATTTTTTATTATTGTTCCAAAAGTAGAAGCTACAGAAGAAATGAAGACTAAATTTACAGTAACGCCTGTTTTACCAGAAAATCAAGTGTCAGGAACATCTAGTTATTATGATTTAATTCTGGCACCAAAGCAATCTTCCACTATTGT'..b'CGTTTCTTGTTGGTTCTTTAATTGCTCATTTTCTTCTTGAAGTTTTTTAAAGGCTGTTTCTTTTTTCTGATAGTAGGCGAGCCTTTCTCTTAACGTCGCCATTTCTTTTTCCTGTTGTTCCGGTTTGATTCCGCTAATTATTTTTTCTGGTTCGAATCCTGGCTGAAAAAAGACTTCTTTTTCAAGCGTATCATCCGAAATATCTTTAATTTTTTTGATTAAACGTCTTTTTGTCATATATATGTCCTTTCTCTCGTCCTTTTAACTAATCACGACAGGCTCCAAATTTGTTTCAAGCGTCTCACGAGCATACGTATCAATGGATTTGACAAGGGTTTGCTCTTGATCTCGATAAGTAAAATTAAAATCAATCATGGTAATTTCTTTAACTGAATTCAACGCTGCAATAAGTGCTACAATATTGTCTTGGCCTGTTTGAAATTCATGGTAACTTAAGCCAACTGAAAAAACAGACAGTGTCAAGGTTTGTGTTTTTTCACTTCTAATCATTGTGATACTCGTCTCTCCGAGGTAAGGACGCCATTCACGCGCTAATTGTAATTCATAATTAGTCAAGACAGCGGCCGATTCTGCCGAAACAGCTTGCTTCCAGGGAAACTGATTTAAGGCTGTTTTTTTAATCGCTTGTTTTTTTATTTTGTCACCTTGAGTAGCTTGGCCTTGTGCCAAACGCTCAATCCGTTGTTCCATGCGGATATTTCGTTGATTTAATTGATAATATGTATAAACAATTCCTAACAATAATACGCTAAGTAGACAAACACTAAACAATAAATAAATCATTAAACGACTATTTTTCTGATACTTATAGAAATTTATTTTCCTCTTTAATGTCCGGTCCTCTGAATCCAGTTTTTCGACAAGTAATCGCAAATACAATTGATAGCTTACAAATAAAAATAAGCAACTACTCATTAAAAGTACAACAATCATCATACAAATATAATCTCCTTTATGTCATCGCTCGACAATCAAAACTTGTAAAATCACCTGTTACGCTCTTTAAAAACTCTATATAGTATTGATTGTAACATTCCGTTTGAGCCTTGCCAACAACTTTATTTAAAATACAATGATAAAATTTTATATTTTATATTTATATTTTAATTTTTAAAATATAAAACAAAAAAAGAGAGATGCCACTTGGCCATCTCTCTCGCTTTTACTCAAACTATGTTTAGCGAACCGTACTAGATCAGTCGCTTTTAAAAAAATCCAATTAGTCTTTGTTGATTTCATAGTAGCTATCGTTCTTTATGTAGCTGAATTTGCTTTTGCTGGGGCTGAATCGCTACTAAGTCCAACACTGATGCCTAAGGCACGATCAACTTCTTCCATAATATCAAGTCTCAAATGACAAACTTTTTCTTTCAAGCGACCCTTATCGATTGTTCGAATCTGCTCTAAAAGAATCACTGAATCTTTTTCAATGCCTGTTTCATCAGAATTAATCCCGATATGTGTTGGCAATTTTGGCTTTGCCATTTTGGCTGTGATCGCCGCAACGATAATCGTTGGGCTAAAATGATTACCTAAGTTATTTTGGACAACAAGGACAGGTCTGACGCCACCTTGTTCCGAGCCCACTACTGGGGAAAGGTCTGCAAAATAAATATCTCCGCGTTTGACCATAGTGGAACCTCCTATCTAGTTATATTCTCTGGGGATTCTTTGTGAGAAAGTACATGCAACTTCATAATGAATGGTTTCTAATTTTTCGGCTACCATTTGTAACGTATTTTCTTCATTGCCATCTTTTCCAACTAATGTAACGACTGAGCCGACAGGAACTTCTTCTGCTAAACGAATCATACATTGATCCATACACACTCGTCCGACGATTTCGCAACGCTTACCATTCACGAGCACTGTAAATCCTTGGAGATGACGCAACCAGCCATCTGCATAGCCGATTGGCACTGTCCCAATCCATTCTTCAGCTTCAGTTACGTAGGTTTCGCCATAGCCAATCCCTTCACCAGCCGCTAAGCGTTTTACATGGATAAGTTCACTGGTCAACCGTAAGGCCGGCTTTAACGCATAGCTTGGGGCAAGCTTATTACCTGAAGGGTTCAATCCATACATGGCTACTCCATAGCGAATCATGTTTCCTGGCACATCAGGATGCCATAACGCTGTCGCACTATTGCTAACATGGACATACCGTGGTAACTCTTCTAAAACTGCTAGAACAGCCTTAAAACGCCCTGCTTGTTTTTCAAAATAGCTTGTATCGATTTCATCAGCTGTTGAAAAATGAGTAAAAATCCCTTCCCATAAAAATTCTTTGTGGGATTGAACAAACCGCACTGCTTGCTTAGTCTCTTCCGGGGTTAAAAAGCCAATCCGTCCCATGCCAGTATCGACTTTTAAGTGAACACGTAATGGCGTGTTACTCTCAGGCGTTAGTTGTTGAAGAGCAGCTTCTAACCATTCTTGTGTAGCTACCGTTACAGACAAATCATATTGAATCAACAAAGGCACATAAGCTAAGTCTACCACACTCAAAATTAAAATGGGGTCCTGAACACCTGCTTCTCTCAATTCAATTGCTTCATCCAATAAGGCGACACAAAAACCTGTCGCGCCACCTTTTTTCGCCGCTTTAGCGGATTCTACGGCGCCATGCCCATAGCCGTTCGCTTTCACAACCGCAAATAAAGCAGTTCCTTCTGGCAAACGTTGACATTCCTTTTGGACATTTTCAGTAATTGCTTGCGTATCGATATGTAACCGTGTAGGACGATGCCATCCAACGACCATTGTACATCCTTCTTTCTTCGTTGCTTCTGTTATTCGCTTTCTAAAACAATTTGTGCAATCGCCATAGTATCTGTGTGCGTAATTGAGACAAACACTTTACCATTATGGGGCGAGTTTGCTACGTATGGTGCACCTGTTTTTTCAGTCAGCACCTCAATATCTTGTAAACCAACTTTACCAATCCCTGTGCCCCATGCTTTAGAAAACGCTTCTTTACAAGCAAAACGACCAGCTAAAAATTCTATTTGACGTTTTGTAGATAACTTTTCAAAAAGGGTCAATTCGTTAGGTGTTAAAACCCGTTGAATAAACGATCCTTGTTTTTCAACAATCGGTTTTATCCGACTTAATTCTACTGCGTCAATACCAATTCCCTTTATCATTTTCCGCCTTACTTCCTATTTAATATAGTTACTCCGAATTACCTTTCATTTTAACAAAATTTCAAAATTTTTCCACTGATTCGCTAAAAAAATAAAGAATGTTTTACAAGATCCTCACACAAATTGAAGTACCATACGTTTTCTTCCTATTTACATTTTTATAAAATTTTTCTGAATTTTTATAAAACGCGAATTGTAAAATTAAGTTAGAAAAATAAAAAGGCATTTATGGTACACTCAAATTGTATTTCCGACGAAAGAAAACAAAGGAGTGTAACCATAAATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAGAATCATATTATCTTCAACATAATAAACCGGTTGAAATCGCTAACCGAATGGGTCGTGCTATACAAACTATTTATAATGTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATTGGCACCAGTATAAAGAAAATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC"}}}, {"name": "contig_graph_path", "file_path": "tests/data/dummy/shovill/contigs.gfa", "hid": "12345", "galaxy_id": "", "content": {}}, {"name": "bam_file_path", "file_path": "tests/data/dummy/shovill/alignment.bam", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/staramr_output.json --- a/test-data/summarize/staramr_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"analysis_software_version": "1.1.0", "reference_database_version": "", "analysis_software_name": "staramr", "results": [{"name": "staramr_report", "file_path": "tests/data/dummy/staramr/resfinder.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "ant(6)-Ia", "Predicted Phenotype": "streptomycin", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "909/909", "Contig": "contig00046", "Start": 4769, "End": 3861, "Accession": "AF330699", "Sequence": "ATGAGATCAGAAAAAGAAATGATGGATTTAGTACTTTCTTTAGCAGAACAGGATGAACGTATTCGAATTGTGACCCTTGAGGGGTCACGCGCAAATATTAATATACCTAAAGATGAATTTCAGGATTATGATATTACATATTTTGTAAGTGATATAGAACCGTTTATATCTAATGATGACTGGCTTAATCAATTTGGGAATATAATAATGATGCAAAAGCCGGAGGATATGGAATTATTCCCACCTGAAGAAAAGGGATTTTCCTATCTTATGCTATTTGATGATTACAATAAAATTGATCTTACCTTATTGCCCTTGGAAGAGTTAGATAATTACCTAAAGGGCGATAAATTAATAAAGGTTCTAATTGATAAAGATTGTAGAATTAAAAGGGACATAGTTCCGACTGATATAGATTATCATGTAAGAAAGCCAAGCGCAAGGGAGTATGATGATTGCTGCAATGAATTTTGGAATGTAACACCTTATGTTATTAAAGGATTGTGCCGTAAGGAAATTTTATTTGCTATTGATCATTTTAATCAGATTGTTCGCCATGAGCTGCTGAGAATGATATCATGGAAGGTCGGCATCGAAACAGGCTTTAAATTAAGTGTAGGCAAGAACTATAAGTTTATTGAAAGGTATATATCCGAGGATTTGTGGGAGAAACTTTTGTCCACCTACCGGATGGATTCCTATGAAAACATATGGGAAGCATTATTTCTATGCCATCAATTGTTCAGGGCGGTATCCGGTGAGGTGGCGGAAAGGCTTCATTATGCCTATCCGGAGTATGATAGGAATATAACAAAATATACCAGGGACATGTATAAAAAATACACTGGTAAAACCGGCTGCCTGGATAGCACATATGCCGCTGATATAGAAGAGAGGCGGGAACAGTGA", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "aph(3\')-III", "Predicted Phenotype": "kanamycin,amikacin", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "795/795", "Contig": "contig00046", "Start": 3229, "End": 2435, "Accession": "M26832", "Sequence": "ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTAAAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAACCTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAAAAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAACGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAAGAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGGCTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTAGCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAAGAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCCGAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGATGGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGACATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTATTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTGGATGAATTGTTTTAG", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "cat(pC221)", "Predicted Phenotype": "chloramphenicol", "Identity": 97.69, "Overlap": 100.0, "HSP Length/Total Length": "648/648", "Contig": "contig00048", "Start": 4344, "End": 4991, "Accession": "X02529", "Sequence": "ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTATTTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTATATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTTATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATTTAG", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "dfrG", "Predicted Phenotype": "trimethoprim", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "498/498", "Contig": "contig00049", "Start": 275, "End": 772, "Accession": "AB205645", "Sequence": "ATGAAAGTTTCTTTGATTGCTGCGATGGATAAGAATAGAGTGATTGGCAAAGAGAATGACATTCCTTGGAGGATTCCCAAGGACTGGGAATATGTTAAAAATACTACAAAGGGACATCCGATAATATTAGGTAGGAAGAACCTTGAATCAATCGGAAGAGCCTTACCTGACAGAAGAAATATTAT'..b'idfinder", "file_path": "tests/data/dummy/staramr/plasmidfinder.tsv", "hid": "12345", "content": [{"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "rep7a", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "939/939", "Contig": "contig00048", "Start": 3276, "End": 4214, "Accession": "X92945", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "rep9b", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "1014/1014", "Contig": "contig00023", "Start": 3630, "End": 4643, "Accession": "CP002494", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "repUS12", "Identity": 99.75, "Overlap": 99.62, "HSP Length/Total Length": "792/795", "Contig": "contig00051", "Start": 918, "End": 127, "Accession": "AF181950", "coverage_ratio": 1.0037878788}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "repUS40", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "1158/1158", "Contig": "contig00026", "Start": 21156, "End": 22313, "Accession": "KP399637", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "repUS43", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "1206/1206", "Contig": "contig00040", "Start": 9430, "End": 8225, "Accession": "CP003584", "coverage_ratio": 1.0}]}, {"name": "pointfinder", "file_path": "tests/data/dummy/staramr/pointfinder.tsv", "hid": "12345", "content": [{"Isolate ID": "SRR1952908", "Gene": "gyrA(S83Y)", "Predicted Phenotype": "ciprofloxacinI/R,nalidixicacid", "Type": "codon", "Position": 83, "Mutation": "TCC->TAC(S->Y)", "Identity": 99.96, "Overlap": 100.0, "HSP Length/Total Length": "2637/2637", "Contig": "contig00008", "Start": 22801, "End": 20165, "coverage_ratio": 1.0}]}, {"name": "settings", "file_path": "tests/data/dummy/staramr/settings.txt", "hid": "12345", "content": {"command_line": "/home/piemari/apps/conda/envs/amr/bin/staramrsearch--nprocs4--no-exclude-genes--pid-threshold95--percent-length-overlap-resfinder90--percent-length-overlap-pointfinder90--percent-length-overlap-plasmidfinder90--output-dir/storage/scratch/piemari/60579242/staramr/staramr_10_Enterococcus_faecalis_S17_L001/storage/scratch/piemari/60579242/staramr/10_Enterococcus_faecalis_S17_L001.fasta", "version": "0.9.1", "start_time": "2023-02-1314:26:11", "end_time": "2023-02-1314:26:13", "total_minutes": "0.04", "resfinder_db_dir": "/home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/resfinder", "resfinder_db_url": "https://bitbucket.org/genomicepidemiology/resfinder_db.git", "resfinder_db_commit": "23661dbb58797b302464855611223b7ba4a21f75", "resfinder_db_date": "Fri,02Dec202211:36", "pointfinder_db_dir": "/home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/pointfinder", "pointfinder_db_url": "https://bitbucket.org/genomicepidemiology/pointfinder_db.git", "pointfinder_db_commit": "a25ac32c7a7a904dff14ffbd17e3b3f7cd732954", "pointfinder_db_date": "Fri,28Oct202210:19", "pointfinder_organisms_all": "campylobacter,enterococcus_faecalis,enterococcus_faecium,escherichia_coli,helicobacter_pylori,klebsiella,mycobacterium_tuberculosis,neisseria_gonorrhoeae,plasmodium_falciparum,salmonella,staphylococcus_aureus", "pointfinder_organisms_valid": "campylobacter,enterococcus_faecalis,enterococcus_faecium,escherichia_coli,helicobacter_pylori,salmonella", "plasmidfinder_db_dir": "/home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/plasmidfinder", "plasmidfinder_db_url": "https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git", "plasmidfinder_db_commit": "b1c9ddac0e618e07630a94452293d84f296a6de5", "plasmidfinder_db_date": "Thu,12Jan202312:51", "mlst_version": "2.23.0", "pointfinder_organism": "None", "pointfinder_gene_drug_version": "072621.1", "resfinder_gene_drug_version": "072621"}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r def7a82d23e1 -r f3233d395549 test-data/summarize/tabular_file_output.json --- a/test-data/summarize/tabular_file_output.json Wed Jul 03 12:07:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"analysis_software_name": "tabular_file", "reference_database_version": "", "analysis_software_version": "", "results": [{"name": "tabular_file_report", "file_path": "tests/data/dummy/tabular_file/report.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"#FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00002", "START": 142975, "END": 143985, "STRAND": "+", "GENE": "bopD", "COVERAGE": "1-1011/1011", "COVERAGE_MAP": "===============", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 98.91, "DATABASE": "vfdb", "ACCESSION": "NP_814691", "PRODUCT": "(bopD)sugar-bindingtranscriptionalregulatorLacIfamily[BopD(VF0362)][EnterococcusfaecalisV583]", "RESISTANCE": null}, {"#FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00003", "START": 7884, "END": 11111, "STRAND": "-", "GENE": "fss3", "COVERAGE": "1-3228/3228", "COVERAGE_MAP": "===============", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.38, "DATABASE": "vfdb", "ACCESSION": "NP_815578", "PRODUCT": "(fss3)EnterococcusfaecalissurfaceproteinFss3fibrinogenbindingprotein[Fibrinogenbindingprotein(AI273)][EnterococcusfaecalisV583]", "RESISTANCE": null}]}], "tool_has_database": false}] \ No newline at end of file |