| Previous changeset 0:6e868bf6c38e (2024-04-30) Next changeset 2:a7387ce2a8ca (2024-07-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834 |
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modified:
macro.xml tooldistillator.xml |
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added:
test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv test-data/amrfinderplus/AMRFinderPlus_report.tsv test-data/summarize/amrfinderplus_output.json |
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| diff -r 6e868bf6c38e -r 65a69de1e294 macro.xml --- a/macro.xml Tue Apr 30 08:42:33 2024 +0000 +++ b/macro.xml Fri May 24 10:47:33 2024 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.8.4.1</token> + <token name="@TOOL_VERSION@">0.8.5.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> |
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| diff -r 6e868bf6c38e -r 65a69de1e294 test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta Fri May 24 10:47:33 2024 +0000 |
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| b'@@ -0,0 +1,209 @@\n+>contig_153_polypolish:4412-4645 strand:- merE broad-spectrum mercury transporter MerE\n+ATGAACAGCCCAGAGCACTTGCCGTCTGAGACGCACAAACCGATCACCGGCTACTTGTGG\n+GGCGCGCTGGCCGTGCTCACCTGTCCCTGCCATTTGCCGATTCTCGCCATTGTGCTAGCC\n+GGCACGACGGCCGGCGCGTTCATCGGGGAGCACTGGGGTATTGCAGCCCTCACGCTGACC\n+GGCTTGTTTGTCCTGTCTGTGACGCGGCTGCTGCGGGCCTTCAAGGGAAGATCA\n+>contig_153_polypolish:7613-7846 strand:- merT mercuric transport protein MerT\n+TCTGAACCACAAAACGGGCGCGGCGCGTTCTTCGCCGGTGGGCTGGCCGCCATTCTTGCG\n+TCGGCCTGCTGCCCGGGGCCGCTGGTTTTGATCGCCTTGGGGTTCAGCGGGGCATGGATC\n+GGCAACCTGACGGTGCTGGAACCCTATCGCCCGATCTTCATCGGCGCAGCGCTGGTCGCG\n+CTGCTTTTCGCCCGGCGGCGCATCTACCGCCCGGCGCAAGCCTGCCAAACCGGG\n+>contig_160_polypolish:86415-86654 strand:- fosA FosA5 family fosfomycin resistance glutathione transferase\n+GCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGTTGGGCATGACGCTG\n+CACGCCCGCTGGGACAGCGGCGCCTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCG\n+CTGGATCCGCAGCGGCGCATCACCCCGCCGGAGGAGAGCGACTACACCCATTATGCGTTT\n+AGCATTAGCGAGGCGGATTTCGCTAGCTTCGCCGCCCGCCTTGAGGTTGCCGGCGTCAGC\n+>contig_30_polypolish:13708-14433 strand:+ blaCTX-M CTX-M family extended-spectrum class A beta-lactamase\n+AAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACA\n+GCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGT\n+AAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAAT\n+CAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCAC\n+GTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAAC\n+GTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCC\n+CGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCC\n+ATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAAT\n+CTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAA\n+GGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCCGGGTTGTGGGG\n+GATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAG\n+ATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCC\n+GTCGCG\n+>contig_30_polypolish:17856-18287 strand:+ merR mercury resistance transcriptional regulator MerR\n+ATGGAAAATAATTTGGAAAACCTGACCATTGGCGTTTTTGCCAAGGCGGCCGGGGTCAAC\n+GTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTAC\n+GGCAGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCA\n+CAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACC\n+CACTGCGAGGAGGCCAGCAGCCCGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATG\n+GCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGC\n+AAGGGGAATGTTTCCTGCCCGTTGATCGCGTCACTACAGGGCGAAGCAGGCCCGGCAAGG\n+TCAGCTATGCCT\n+>contig_30_polypolish:20698-21348 strand:+ catA1 type A-1 chloramphenicol O-acetyltransferase\n+GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTT\n+GAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACG\n+GCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATT\n+CTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTG\n+GTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTT\n+TCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAA\n+GATGTGGCGTGTTACGGTGAAAACCGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGT\n+TTTTCGTCTCAGCCAATCCCACGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAAT\n+ATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAG\n+GTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGC\n+AGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCG\n+>contig_30_polypolish:3018-3344 strand:+ merR mercury resistance transcriptional regulator MerR\n+TTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTG\n+TTGCGGGAACCGGACAAGCCTTACGGCGGCATCCGCCGCTATGGGGAGGCGGACGTGGTT\n+CGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAG\n+CTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCTTGGCCGAACACAAG\n+CTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAA\n+CTCGTGTGCGCCTGCCATGCACGAAGG\n+>contig_30_polypolish:5821-6243 strand:+ catA1 type A-1 chloramphenicol O-acetyltransferase\n+GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTT\n+GAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACG\n+GCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATT\n+CTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTG\n+GTGATATGGGATAGTGTTCA'..b"C\n+TTCTCGGCGAACGCGCTGGGTTGGTTCAGTCATCGGCAATGGCTGCGCAGTCTGCTCGGC\n+ATGATCGGCCCGGCCATCGTGTTTGCGGCCACGGTCTGGCTGCTCGGCAACTGGTGGACG\n+GCGAACCTGATGTACGTCGGCACCGGCCTT\n+>contig_39_polypolish:3496-3825 strand:- qacE quaternary ammonium compound efflux SMR transporter QacE\n+ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCA\n+TTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTAT\n+GGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTAT\n+GCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGG\n+CAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTT\n+TTAAACTTGCTTTCCAAAGCAAGTGCCCAC\n+>contig_39_polypolish:4010-4327 strand:- dfrA30 trimethoprim-resistant dihydrofolate reductase DfrA30\n+GGGGCGCTCCCCAATAGGAAATACGCGGTCGTTACTCGCTCAGCTCGGACGGCCAATAAT\n+GACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCACC\n+GGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCT\n+ACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATT\n+CCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTAT\n+CAAATTTGGAAAAAGGGT\n+>contig_40_polypolish:2574-3359 strand:+ aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib\n+ATATTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGAT\n+TTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGC\n+GGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGC\n+CCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATT\n+CCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATG\n+GGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGTTTGAGCGCAGG\n+CTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGAC\n+TTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGA\n+GAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCC\n+TGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTT\n+GGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAA\n+GAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTG\n+GGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACT\n+TGGGGT\n+>contig_40_polypolish:3555-4103 strand:+ aph(6)-Id aminoglycoside O-phosphotransferase APH(6)-Id\n+GGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAG\n+CGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCGAGCGACCGAAATTGCAGCG\n+GAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCG\n+ATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGT\n+CAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAA\n+CTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGG\n+CTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTC\n+TACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCG\n+GACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCGTGCGTACGCT\n+TATGGGTGC\n+>contig_40_polypolish:632-1258 strand:+ aph(3')-Ia aminoglycoside O-phosphotransferase APH(3')-Ia\n+ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACATGGAT\n+GCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATC\n+TATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGC\n+GTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCT\n+CTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCG\n+ATCCCCGGGAAAACAGCATTCCGGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATT\n+GTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCT\n+TTTAACAACGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTG\n+GTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAA\n+GAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCA\n+CTTGATAACCTTATTTTTGACGAGGGA\n+>contig_41_polypolish:100023-100541 strand:- terD tellurium resistance membrane protein TerD\n+ATGAGCGTTTCACTATCTAAAGGCGGCAACGTTTCCCTGAGCAAAACCGCGCCAAGCATG\n+AAAAACGTGCTGGTTGGCCTTGGCTGGGATGCACGTTCTACGGACGGTCAGGACTTTGAC\n+CTCGATGCTTCCGCATTTCTGCTGGCAGCCAATGGCAAGGTTCGTGGCGATGCAGATTTC\n+ATTTTCTATAACAACCTGAAATCTGCTGATGGTTCCGTTACTCATACCGGTGATAACCGT\n+ACCGGTGAAGGTGATGGCGACGATGAATCCCTCAAAATCAAACTGGACGCGGTACACGGG\n+GATGTCGACAAAATTATTTTCGTTGTCACTATCCATGATGCTCAGGCTCGTCGCCAGAGC\n+TTCGGTCAGGTTTCCGGCGCATTTATCCGTCTGGTGAATGATGACAATCAGACTGAAGTT\n+GCTCGCTACGATCTGACAGAAGACGCTTCTACTGAAACTGCCATGCTGTTTGGGGAGCTG\n+TATCGTCACAACGGAGAATGGAAATTCCGTGCGGTTGGC\n" |
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| diff -r 6e868bf6c38e -r 65a69de1e294 test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv Fri May 24 10:47:33 2024 +0000 |
| [ |
| @@ -0,0 +1,35 @@ +Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description Hierarchy node +NA contig_107_polypolish 5 861 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.82 869 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.95 870 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.82 869 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.95 870 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.82 869 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.95 870 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 345 1334 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 345 1334 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 345 1334 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 416 1334 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 416 1334 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 416 1334 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1319 2308 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1319 2308 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1319 2308 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1390 2308 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1390 2308 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1390 2308 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.01 417 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.30 418 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.01 417 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.30 418 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39847 40836 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39847 40836 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39847 40836 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39918 40836 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39918 40836 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39918 40836 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 31987 + 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 31987 + 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 31987 + 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 32058 + 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 32058 + 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 32058 + 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA |
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| diff -r 6e868bf6c38e -r 65a69de1e294 test-data/amrfinderplus/AMRFinderPlus_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus/AMRFinderPlus_report.tsv Fri May 24 10:47:33 2024 +0000 |
| b |
| b'@@ -0,0 +1,58 @@\n+Protein identifier\tContig id\tStart\tStop\tStrand\tGene symbol\tSequence name\tScope\tElement type\tElement subtype\tClass\tSubclass\tMethod\tTarget length\tReference sequence length\t% Coverage of reference sequence\t% Identity to reference sequence\tAlignment length\tAccession of closest sequence\tName of closest sequence\tHMM id\tHMM description\tHierarchy node\n+NA\tcontig_153_polypolish\t4412\t4645\t-\tmerE\tbroad-spectrum mercury transporter MerE\tplus\tSTRESS\tMETAL\tMERCURY\tMERCURY\tBLASTX\t78\t78\t100.00\t96.15\t78\tAAC38236.1\tbroad-spectrum mercury transporter MerE\tNA\tNA\tmerE\n+NA\tcontig_153_polypolish\t7613\t7846\t-\tmerT\tmercuric transport protein MerT\tplus\tSTRESS\tMETAL\tMERCURY\tMERCURY\tPARTIALX\t78\t116\t67.24\t92.31\t78\tCAA70196.1\tmercuric transport protein MerT\tNA\tNA\tmerT\n+NA\tcontig_160_polypolish\t86415\t86654\t-\tfosA\tFosA5 family fosfomycin resistance glutathione transferase\tcore\tAMR\tAMR\tFOSFOMYCIN\tFOSFOMYCIN\tPARTIALX\t80\t139\t57.55\t98.75\t80\tWP_114473955.1\tfosfomycin resistance glutathione transferase FosA9\tNA\tNA\tfosA5_fam\n+NA\tcontig_30_polypolish\t3018\t3344\t+\tmerR\tmercury resistance transcriptional regulator MerR\tplus\tSTRESS\tMETAL\tMERCURY\tMERCURY\tPARTIALX\t109\t144\t75.69\t93.58\t109\tBAA20334.1\tmercury resistance transcriptional regulator MerR\tNA\tNA\tmerR_Ps\n+NA\tcontig_30_polypolish\t5821\t6243\t+\tcatA1\ttype A-1 chloramphenicol O-acetyltransferase\tcore\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tPARTIALX\t141\t219\t64.38\t98.58\t141\tWP_000412211.1\ttype A-1 chloramphenicol O-acetyltransferase\tNA\tNA\tcatA1\n+NA\tcontig_30_polypolish\t5821\t6243\t+\tcatA1\ttype A-1 chloramphenicol O-acetyltransferase\tcore\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tPARTIALX\t141\t219\t64.38\t98.58\t141\tWP_063843217.1\ttype A-1 chloramphenicol O-acetyltransferase\tNA\tNA\tcatA1\n+NA\tcontig_30_polypolish\t13708\t14433\t+\tblaCTX-M\tCTX-M family extended-spectrum class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tCEPHALOSPORIN\tINTERNAL_STOP\t242\t291\t84.54\t90.24\t246\tWP_063860025.1\textended-spectrum class A beta-lactamase CTX-M-179\tNA\tNA\tblaCTX-M\n+NA\tcontig_30_polypolish\t17856\t18287\t+\tmerR\tmercury resistance transcriptional regulator MerR\tplus\tSTRESS\tMETAL\tMERCURY\tMERCURY\tBLASTX\t144\t144\t100.00\t92.36\t144\tCAA77320.1\tmercury resistance transcriptional regulator MerR\tNA\tNA\tmerR_Ps\n+NA\tcontig_30_polypolish\t20698\t21348\t+\tcatA1\ttype A-1 chloramphenicol O-acetyltransferase\tcore\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tBLASTX\t217\t219\t99.09\t92.17\t217\tWP_000412211.1\ttype A-1 chloramphenicol O-acetyltransferase\tNA\tNA\tcatA1\n+NA\tcontig_35_polypolish\t4787\t5644\t-\taac(3)-IIe\taminoglycoside N-acetyltransferase AAC(3)-IIe\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tGENTAMICIN\tEXACTX\t286\t286\t100.00\t100.00\t286\tWP_000557452.1\taminoglycoside N-acetyltransferase AAC(3)-IIe\tNA\tNA\taac(3)-IIe\n+NA\tcontig_36_polypolish\t9168\t9608\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t147\t286\t51.40\t99.32\t147\tWP_002904004.1\textended-spectrum class A beta-lactamase SHV-12\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9168\t9608\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t147\t286\t51.40\t99.32\t147\tWP_004176269.1\tbroad-spectrum class A beta-lactamase SHV-11\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9168\t9608\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t147\t286\t51.40\t99.32\t147\tWP_004183952.1\tbroad-spectrum class A beta-lactamase SHV-60\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9168\t9608\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t147\t286\t51.40\t99.32\t147\tWP_032488413.1\textended-spectrum class A beta-lactamase SHV-2a\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9168\t9608\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t147\t286\t51.40\t99.32\t147\tWP_032494802.1\textended-spectrum class A beta-lactamase SHV-129\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9168\t9608\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t147\t286\t51.40\t99.32\t147\tWP_063864610.1\tinhibitor-resistant broad-spectrum c'..b"mase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t146\t286\t51.05\t95.89\t146\tWP_063864692.1\textended-spectrum class A beta-lactamase SHV-55\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9587\t10024\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t146\t286\t51.05\t95.89\t146\tWP_063864698.1\textended-spectrum class A beta-lactamase SHV-64\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9587\t10024\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t146\t286\t51.05\t95.89\t146\tWP_063864700.1\textended-spectrum class A beta-lactamase SHV-66\tNA\tNA\tblaSHV\n+NA\tcontig_36_polypolish\t9587\t10024\t+\tblaSHV\tSHV family class A beta-lactamase\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tPARTIALX\t146\t286\t51.05\t95.89\t146\tWP_268871888.1\tclass A beta-lactamase SHV-230\tNA\tNA\tblaSHV\n+NA\tcontig_37_polypolish\t18\t569\t+\taac(6')-Ib3\taminoglycoside N-acetyltransferase AAC(6')-Ib3\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMIKACIN/KANAMYCIN/TOBRAMYCIN\tALLELEX\t184\t184\t100.00\t100.00\t184\tWP_032488579.1\taminoglycoside N-acetyltransferase AAC(6')-Ib3\tNA\tNA\taac(6')-Ib3\n+NA\tcontig_37_polypolish\t642\t1424\t+\taadA1\tANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tSTREPTOMYCIN\tBLASTX\t261\t262\t100.00\t97.71\t262\tWP_001206315.1\tANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1\tNA\tNA\taadA1\n+NA\tcontig_37_polypolish\t3006\t3863\t+\tblaTEM-1\tbroad-spectrum class A beta-lactamase TEM-1\tcore\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tALLELEX\t286\t286\t100.00\t100.00\t286\tWP_000027057.1\tbroad-spectrum class A beta-lactamase TEM-1\tNA\tNA\tblaTEM-1\n+NA\tcontig_37_polypolish\t8924\t9133\t-\tmerC\torganomercurial transporter MerC\tplus\tSTRESS\tMETAL\tMERCURY\tORGANOMERCURY\tPARTIALX\t70\t140\t50.00\t90.00\t70\tAAC33908.1\torganomercurial transporter MerC\tNA\tNA\tmerC\n+NA\tcontig_39_polypolish\t3496\t3825\t-\tqacE\tquaternary ammonium compound efflux SMR transporter QacE\tcore\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tEXACTX\t110\t110\t100.00\t100.00\t110\tWP_010890145.1\tquaternary ammonium compound efflux SMR transporter QacE\tNA\tNA\tqacE\n+NA\tcontig_39_polypolish\t4010\t4327\t-\tdfrA30\ttrimethoprim-resistant dihydrofolate reductase DfrA30\tcore\tAMR\tAMR\tTRIMETHOPRIM\tTRIMETHOPRIM\tPARTIALX\t106\t157\t67.52\t98.11\t106\tWP_063844408.1\ttrimethoprim-resistant dihydrofolate reductase DfrA30\tNA\tNA\tdfrA30\n+NA\tcontig_40_polypolish\t632\t1258\t+\taph(3')-Ia\taminoglycoside O-phosphotransferase APH(3')-Ia\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tKANAMYCIN\tPARTIALX\t209\t271\t77.12\t99.04\t209\tWP_000018329.1\taminoglycoside O-phosphotransferase APH(3')-Ia\tNA\tNA\taph(3')-Ia\n+NA\tcontig_40_polypolish\t632\t1258\t+\taph(3')-Ia\taminoglycoside O-phosphotransferase APH(3')-Ia\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tKANAMYCIN\tPARTIALX\t209\t271\t77.12\t99.04\t209\tWP_063842148.1\taminoglycoside O-phosphotransferase APH(3')-Ia\tNA\tNA\taph(3')-Ia\n+NA\tcontig_40_polypolish\t2574\t3359\t+\taph(3'')-Ib\taminoglycoside O-phosphotransferase APH(3'')-Ib\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tSTREPTOMYCIN\tBLASTX\t262\t267\t98.13\t100.00\t262\tWP_001082319.1\taminoglycoside O-phosphotransferase APH(3'')-Ib\tNA\tNA\taph(3'')-Ib\n+NA\tcontig_40_polypolish\t3555\t4103\t+\taph(6)-Id\taminoglycoside O-phosphotransferase APH(6)-Id\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tSTREPTOMYCIN\tPARTIALX\t183\t278\t65.83\t98.91\t183\tWP_000480968.1\taminoglycoside O-phosphotransferase APH(6)-Id\tNA\tNA\taph(6)-Id\n+NA\tcontig_40_polypolish\t3555\t4103\t+\taph(6)-Id\taminoglycoside O-phosphotransferase APH(6)-Id\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tSTREPTOMYCIN\tPARTIALX\t183\t278\t65.83\t98.91\t183\tWP_000480972.1\taminoglycoside O-phosphotransferase APH(6)-Id\tNA\tNA\taph(6)-Id\n+NA\tcontig_40_polypolish\t3555\t4103\t+\taph(6)-Id\taminoglycoside O-phosphotransferase APH(6)-Id\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tSTREPTOMYCIN\tPARTIALX\t183\t278\t65.83\t98.91\t183\tWP_063842183.1\taminoglycoside O-phosphotransferase APH(6)-Id\tNA\tNA\taph(6)-Id\n+NA\tcontig_41_polypolish\t100023\t100541\t-\tterD\ttellurium resistance membrane protein TerD\tplus\tSTRESS\tMETAL\tTELLURIUM\tTELLURIUM\tBLASTX\t173\t192\t90.10\t98.84\t173\tAAA98292.1\ttellurium resistance membrane protein TerD\tNA\tNA\tterD\n" |
| b |
| diff -r 6e868bf6c38e -r 65a69de1e294 test-data/summarize/amrfinderplus_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/amrfinderplus_output.json Fri May 24 10:47:33 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\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 6e868bf6c38e -r 65a69de1e294 tooldistillator.xml --- a/tooldistillator.xml Tue Apr 30 08:42:33 2024 +0000 +++ b/tooldistillator.xml Fri May 24 10:47:33 2024 +0000 |
| b |
| b'@@ -20,7 +20,16 @@\n \'$tool.select_tool.input\'\n --analysis_software_version \'$tool.select_tool.analysis_software_version\'\n --reference_database_version \'$tool.select_tool.reference_database_version\'\n- #if $tool.select_tool.tool_list == \'bakta\'\n+ #if $tool.select_tool.tool_list == \'amrfinderplus\':\n+ #if $tool.select_tool.point_mutation_report_path\n+ --point_mutation_report_path \'$tool.select_tool.point_mutation_report_path\'\n+ --point_mutation_report_hid \'$tool.select_tool.point_mutation_report_path.hid\'\n+ #end if\n+ #if $tool.select_tool.nucleotide_sequence_path\n+ --nucleotide_sequence_path \'$tool.select_tool.nucleotide_sequence_path\'\n+ --nucleotide_sequence_hid \'$tool.select_tool.nucleotide_sequence_path.hid\'\n+ #end if\n+ #elif $tool.select_tool.tool_list == \'bakta\'\n #if $tool.select_tool.annotation_tabular_path\n --annotation_tabular_path \'$tool.select_tool.annotation_tabular_path\'\n --annotation_tabular_hid \'$tool.select_tool.annotation_tabular_path.hid\'\n@@ -191,21 +200,22 @@\n <repeat name="tools" title="Tool" min="0">\n <conditional name="select_tool">\n <param name="tool_list" type="select" label="Available tools">\n- <option value="abricate">abricate</option>\n- <option value="bakta">bakta</option>\n- <option value="bandage">bandage</option>\n- <option value="bracken">bracken</option>\n- <option value="fastp">fastp</option>\n- <option value="integronfinder2">integronfinder2</option>\n- <option value="isescan">isescan</option>\n- <option value="kraken2">kraken2</option>\n+ <option value="abricate">Abricate</option>\n+ <option value="amrfinderplus">AMRFinderPlus</option>\n+ <option value="bakta">Bakta</option>\n+ <option value="bandage">Bandage</option>\n+ <option value="bracken">Bracken</option>\n+ <option value="fastp">Fastp</option>\n+ <option value="integronfinder2">Integronfinder2</option>\n+ <option value="isescan">ISEScan</option>\n+ <option value="kraken2">Kraken2</option>\n <option value="multiqc">MultiQC</option>\n- <option value="plasmidfinder">plasmidfinder</option>\n- <option value="quast">quast</option>\n- <option value="recentrifuge">recentrifuge</option>\n- <option value="refseqmasher">refseqmasher</option>\n- <option value="shovill">shovill</option>\n- <option value="staramr">staramr</option>\n+ <option value="plasmidfinder">PlasmidFinder</option>\n+ <option value="quast">Quast</option>\n+ <option value="recentrifuge">Recentrifuge</option>\n+ <option value="refseqmasher">RefSeqMasher</option>\n+ <option value="shovill">Shovill</option>\n+ <option value="staramr">Staramr</option>\n <option value="tabular_file">tabular_generic_file</option>\n </param>\n <when value="abricate">\n@@ -213,6 +223,13 @@\n <expand macro="analysis_software_version"/>\n <expand macro="reference_database_version"/>\n </when>\n+ <when value="amrfinderplus">\n+ <param name="input" type="data" format="tabular" multiple="false" label="AMRFinderPlus report file" help="Tabular file from AMRFinderPlus'..b't_assert" name="plasmidfinder_9_output" text="repUS40_1_repB"/>\n+ <expand macro="element_assert" name="quast_10_output" text="2944723"/>\n+ <expand macro="element_assert" name="recentrifuge_11_output" text="6.4917947578"/>\n+ <expand macro="element_assert" name="refseqmasher_12_output" text="GCF_000519925.1"/>\n+ <expand macro="element_assert" name="shovill_13_output" text="436224"/>\n+ <expand macro="element_assert" name="staramr_14_output" text="10_Enterococcus_faecalis_S17_L001"/>\n+ <expand macro="element_assert" name="tabular_file_15_output" text="NP_814691"/>\n </output_collection>\n </test>\n \n@@ -596,12 +624,15 @@\n This tool here is extracting information from output files of specific tools and exposing it as JSON files\n ** Tool input**\n \n-ToolDistillator can use several input type from at least 14 different tools :\n+ToolDistillator can use several input type from at least 15 different tools :\n \n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Tools | Version | Default input file| Optional files |\n++----------------+----------------+-------------------+------------------------------------------------------------+\n | Abricate | 1.0.1 | output.tsv | |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n+| AMRFinderPlus | 3.11.26 | report.tsv | point_mutation_report.tsv, nucleotide_sequence.fasta |\n++----------------+----------------+-------------------+------------------------------------------------------------+\n | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt |\n +----------------+----------------+-------------------+------------------------------------------------------------+ \n | Bandage | 0.8.1 | info.txt | |\n@@ -616,13 +647,13 @@\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n-| Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta |\n+| PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Quast | 5.2.0 | output.tsv | |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n-| Refseqmasher | 0.1.2 | output.tsv | |\n+| RefSeqMasher | 0.1.2 | output.tsv | |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n' |