| Previous changeset 1:da5f1924bb2e (2022-09-16) Next changeset 3:865ece5ca178 (2023-02-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c |
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modified:
bakta.xml macro.xml tool-data/bakta_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p test-data/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab test-data/amrfinderplus-db/2021-09-30.1/AMRProt-suppress test-data/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab test-data/amrfinderplus-db/2021-09-30.1/AMRProt.pdb test-data/amrfinderplus-db/2021-09-30.1/AMRProt.phr test-data/amrfinderplus-db/2021-09-30.1/AMRProt.pin test-data/amrfinderplus-db/2021-09-30.1/AMRProt.psq test-data/amrfinderplus-db/2021-09-30.1/AMRProt.ptf test-data/amrfinderplus-db/2021-09-30.1/AMRProt.pto test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.not test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto test-data/amrfinderplus-db/2021-09-30.1/database_format_version.txt test-data/amrfinderplus-db/2021-09-30.1/fam.tab test-data/amrfinderplus-db/2021-09-30.1/taxgroup.tab test-data/amrfinderplus-db/2021-09-30.1/version.txt test-data/amrfinderplus_database.loc test-data/bakta_database.loc tool-data/amrfinderplus_database.loc.sample |
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removed:
test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.phr test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pin test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.psq test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.ptf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pto test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto test-data/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt test-data/test-db/amrfinderplus-db/2021-09-30.1/fam.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/version.txt test-data/test_database.loc |
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| diff -r da5f1924bb2e -r debdc1469b41 bakta.xml --- a/bakta.xml Fri Sep 16 13:42:15 2022 +0000 +++ b/bakta.xml Wed Dec 21 20:59:54 2022 +0000 |
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| b'@@ -11,6 +11,10 @@\n <expand macro="version_command"/>\n \n <command detect_errors="aggressive"><![CDATA[\n+ mkdir ./database_path &&\n+ ln -s \'$(input_option.bakta_db_select.fields.path)/\'* database_path &&\n+ ln -s \'$(input_option.amrfinder_db_select.fields.path)\' database_path &&\n+\n bakta\n #*======================================\n CPU option\n@@ -19,7 +23,7 @@\n #*======================================\n Bakta database\n ======================================*#\n- --db $input_option.db_select.fields.path\n+ --db ./database_path\n #if $input_option.min_contig_length\n --min-contig-length $input_option.min_contig_length\n #else if $annotation.compliant\n@@ -71,36 +75,7 @@\n skip some step of the bakta analysis\n ======================================*#\n \n- #if "skip_trna" in $workflow.skip_analysis\n- --skip-trna\n- #end if\n- #if "skip_tmrna" in $workflow.skip_analysis\n- --skip-tmrna\n- #end if\n- #if "skip_rrna" in $workflow.skip_analysis\n- --skip-rrna\n- #end if\n- #if "skip_ncrna" in $workflow.skip_analysis\n- --skip-ncrna\n- #end if\n- #if "skip_ncrna_region" in $workflow.skip_analysis\n- --skip-ncrna-region\n- #end if\n- #if "skip_crispr" in $workflow.skip_analysis\n- --skip-crispr\n- #end if\n- #if "skip_cds" in $workflow.skip_analysis\n- --skip-cds\n- #end if\n- #if "skip_sorf" in $workflow.skip_analysis\n- --skip-sorf\n- #end if\n- #if "skip_gap" in $workflow.skip_analysis\n- --skip-gap\n- #end if\n- #if "skip_ori" in $workflow.skip_analysis\n- --skip-ori\n- #end if\n+ #echo " ".join($workflow.skip_analysis)\n \n #*======================================\n Genome file\n@@ -114,11 +89,18 @@\n <inputs>\n <!-- DB and file INPUT -->\n <section name="input_option" title="Input/Output options" expanded="true">\n- <param name="db_select" type="select" label="The bakta database">\n+ <param name="bakta_db_select" type="select" label="The bakta database">\n <options from_data_table="bakta_database">\n- <validator message="No bakta database is available" type="no_options"/>\n+ <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/>\n+ <validator message="No bakta database is available" type="no_options"/>\n </options>\n </param>\n+ <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">\n+ <options from_data_table="amrfinderplus_database">\n+ <validator message="No amrfinderplus database is available" type="no_options"/>\n+ </options>\n+ </param>\n+\n <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/>\n <param name="min_contig_length" type="integer" optional="true" min="0" label="Minimum contig size" help="Minimum contig size (default = 1; 200 in compliant mode) (--min-contig-length)"/>\n </section>\n@@ -158,41 +140,43 @@\n <!-- PARAMETER FOR WORKFLOW ANALYSIS -->\n <section name="workflow" title="Workflow option to skip steps">\n <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">\n- <option value="skip_trna"> Skip tRNA detection and annotation </option>\n- <option value="skip_tmrna"> Skip tmRNA detection and annotation </option>\n- <option value="skip_rrna"> Skip rRNA detection and annotation </option>\n- <option value="skip_ncrna"> Skip ncRNA detection and annotation </option>\n- '..b' </section>\n- <section name="output_files">\n- <param name="output_selection" value="log_txt,sum_txt"/>\n- </section>\n- <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="4"/>\n- <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>\n- </test>\n+ <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/>\n+ <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/>\n+ <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/>\n+ <output name="annotation_plot">\n+ <assert_contents>\n+ <has_size value="418399" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="4"> <!-- TEST_4 annotations -->\n+ <section name="input_option" >\n+ <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n+ <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n+ <param name="input_file" value="NC_002127.1.fna"/>\n+ </section>\n+ <section name="annotation">\n+ <param name="complete" value="true"/>\n+ <param name="prodigal" value="prodigal.tf"/>\n+ <param name="translation_table" value="4"/>\n+ <param name="replicons" value="replicons.tsv"/>\n+ <param name="compliant" value="true"/>\n+ <param name="proteins" value="user-proteins.faa"/>\n+ </section>\n+ <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>\n+ <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>\n+ <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>\n+ <output name="annotation_plot">\n+ <assert_contents>\n+ <has_size value="418399" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->\n+ <section name="input_option" >\n+ <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n+ <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n+ <param name="input_file" value="NC_002127.1.fna"/>\n+ </section>\n+ <section name="annotation">\n+ <param name="complete" value="true"/>\n+ <param name="translation_table" value="4"/>\n+ </section>\n+ <section name="workflow">\n+ <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori"/>\n+ </section>\n+ <section name="output_files">\n+ <param name="output_selection" value="log_txt,sum_txt"/>\n+ </section>\n+ <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/>\n+ <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>\n+ </test>\n </tests>\n <help><![CDATA[**What it does**\n Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.\n@@ -465,7 +388,7 @@\n \n **Annotation options**\n 1. You can specify if all sequences (chromosome or plasmids) are complete or not\n- 2. You can add your own prodigal traingin file for CDS prediction\xc5\x93\n+ 2. You can add your own prodigal training file for CDS prediction\xc5\x93\n 3. The translation table could be modified, default is the 11th for bacteria\n 4. You can specify if bacteria is gram -/+ or unknonw (default value unknow)\n 5. You can keep the name of contig present in the input file\n' |
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| diff -r da5f1924bb2e -r debdc1469b41 macro.xml --- a/macro.xml Fri Sep 16 13:42:15 2022 +0000 +++ b/macro.xml Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -1,5 +1,7 @@ + <macros> - <token name="@TOOL_VERSION@">1.5.0</token> + <token name="@TOOL_VERSION@">1.6.1</token> + <token name="@BAKTA_VERSION@">1.5</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#taxgroup accession_version mutation_position mutation_symbol class subclass mutated_protein_name +Escherichia WP_000019358.1 12 soxS_A12S MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus-db/2021-09-30.1/AMRProt-suppress --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/2021-09-30.1/AMRProt-suppress Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#taxgroup protein_accession protein_gi +Escherichia AAA21095.1 151858 |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name +Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus-db/2021-09-30.1/database_format_version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/2021-09-30.1/database_format_version.txt Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,1 @@ +3.10.16 |
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| b'@@ -0,0 +1,1744 @@\n+#node_id\tparent_node_id\tgene_symbol\thmm_id\thmm_tc1\thmm_tc2\tblastrule_complete_ident\tblastrule_complete_wp_coverage\tblastrule_complete_br_coverage\tblastrule_partial_ident\tblastrule_partial_wp_coverage\tblastrule_partial_br_coverage\treportable\ttype\tsubtype\tclass\tsubclass\tfamily_name\n+ACID\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tACID\t\t\t\n+ALL\t\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\t\t\t\t\t\n+AME\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\n+AMR\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n+BIOCIDE\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tBIOCIDE\t\t\t\n+BcII\tbla-B1\tbla2\tNF033095.1\t500.00\t500.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tCARBAPENEM\tBcII family subclass B1 metallo-beta-lactamase\n+CDF_efflux\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\n+CMY2-MIR-ACT-EC\tbla-C\tampC\tNF012173.1\t680.00\t680.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tCMY2/MIR/ACT/EC family class C beta-lactamase\n+EFFLUX\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tefflux\n+HARLDQ_not_B3\tbla-B3\t-\tNF000405.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tHARLDQ motif MBL-fold protein\n+HEAT\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tHEAT\t\t\t\n+HTH_5\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\n+LHR_hdeD\tHEAT\thdeD-GI\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\n+LHR_hsp20A\tHEAT\thsp20\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\n+LHR_hsp20B\tHEAT\tshsP\t-\t0.00\t0.00\t93.00\t90.00\t90.00\t94.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\n+LHR_kefB\tHEAT\tkefB-GI\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\n+LHR_psiE\tHEAT\tpsi-GI\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\n+LHR_trx\tHEAT\ttrxLHR\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\n+LHR_yfdX1\tHEAT\tyfdX1\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\n+LHR_yfdX2\tHEAT\tyfdX2\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\n+MATE_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\n+METAL-RND-IM\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\n+METAL\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tMetal Resistance\n+MFS_efflux_CHL\tMFS_efflux\tcml\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\n+MFS_efflux_qac\tBIOCIDE\tqac\tNF000089.1\t900.00\t900.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQacA/B family quaternary ammonium compound efflux MFS transporter\n+MFS_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\n+MerP_Gneg\tmerP\tmerP\tTIGR02052.1\t92.55\t92.55\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tMETAL\tMERCURY\tMERCURY\tmercury resistance system periplasmic binding protein MerP\n+OM_sidero\tVIRULENCE_Ecoli\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\n+P-type_ATPase\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\n+PERI-SENSOR\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\n+RESPONSE_REG\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tDNA-binding response regulator\n+RND-IM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux RND transporter permease subunit\n+RND-OM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug'..b'ferase Vat(A)\n+vat(B)\tvat\tvat(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(B)\n+vat(C)\tvat\tvat(C)\tNF000097.1\t425.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(C)\n+vat(D)\tvat\tvat(D)\tNF000111.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(D)\n+vat(E)\tvat\tvat(E)\tNF000020.1\t450.00\t450.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(E)\n+vat(F)\tvat\tvat(F)\tNF000147.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(F)\n+vat(H)\tvat\tvat(H)\tNF000504.1\t475.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(H)\n+vat(I)\tvat\tvatI\tNF033468.1\t415.00\t415.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(I)\n+vat\tAMR\tvat\tNF000311.1\t300.00\t300.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tVat family streptogramin A O-acetyltransferase\n+vga(A)\tvga\tvga(A)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(A)\n+vga(B)\tvga\tvga(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(B)\n+vga(C)\tvga\tvga(C)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(C)\n+vga(D)\tvga\tvga(D)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(D)\n+vga(E)\tvga\tvga(E)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(E)\n+vga\tabc-f\tvga\tNF000170.1\t800.00\t800.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tVga family ABC-F type ribosomal protection protein\n+vgb(A)\tvgb\tvgb(A)\tNF000022.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(A)\n+vgb(B)\tvgb\tvgb(B)\tNF000096.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(B)\n+vgb(C)\tvgb\tvgbC\t-\t0.00\t0.00\t84.00\t90.00\t90.00\t88.00\t90.00\t25.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(C)\n+vgb\tAMR\tvgb\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase\n+virF\tVIRULENCE_Ecoli\tvirF\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tAraC family invasion system transcriptional regulator VirF\n+vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tMACROLIDE/PLEUROMUTILIN\tLINCOSAMIDE/STREPTOGRAMIN/TIAMULIN\tABC-F type ribosomal protection protein VmlR\n+vph\tAMR\tvph\tNF000088.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tTUBERACTINOMYCIN\tVIOMYCIN\tviomycin phosphotransferase\n+ybtP\tVIRULENCE\tybtP\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtP\n+ybtQ\tVIRULENCE\tybtQ\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtQ\n+yfeA\tVIRULENCE\tyfeA\t-\t0.00\t0.00\t83.00\t90.00\t90.00\t88.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter substrate-binding protein YfeA\n+yfeB\tVIRULENCE\tyfeB\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter ATP-binding protein YfeB\n+yfeD\tVIRULENCE\tyfeD\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t92.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter permease subunit YfeD\n+zbmA\tble\tzbmA\tNF000479.1\t280.00\t280.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBLEOMYCIN\tZORBAMYCIN\tzorbamycin binding protein ZbmA\n' |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus-db/2021-09-30.1/taxgroup.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/2021-09-30.1/taxgroup.tab Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#taxgroup gpipe_taxgroup number_of_nucl_ref_genes +Acinetobacter_baumannii Acinetobacter 0 |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus-db/2021-09-30.1/version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/2021-09-30.1/version.txt Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,1 @@ +2021-09-30.1 |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 test-data/amrfinderplus_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus_database.loc Wed Dec 21 20:59:54 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, path +# +# for example +amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db +amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/bakta_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta_database.loc Wed Dec 21 20:59:54 2022 +0000 |
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| @@ -0,0 +1,11 @@ +# Tab separated with 4 columns: +# value : unique value used to generate the database path provided from the zenodo DOI +# dbkey : name of the database generate using the date and version of the bakta database +# bakta_version : tool version to filter database version depending of the tool +# path : final oath to bakta database on galaxy +# value, dbkey, bakta_version, path +# eg. +# 7025248 V4.0_2022-08-29 1.5 path/to/db +V0.0_date_test 7190015 1.5 ${__HERE__}/test-db +V0.1_2022-08-29 7197216 1.5 ${__HERE__}/test-db +V0.2_2022-08-19 7197217 1.7 ${__HERE__}/test-db |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p |
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| Binary file test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p has changed |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#taxgroup accession_version mutation_position mutation_symbol class subclass mutated_protein_name -Escherichia WP_000019358.1 12 soxS_A12S MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup protein_accession protein_gi -Escherichia AAA21095.1 151858 |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name -Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -3.10.16 |
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| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/fam.tab --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/fam.tab Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1744 +0,0 @@\n-#node_id\tparent_node_id\tgene_symbol\thmm_id\thmm_tc1\thmm_tc2\tblastrule_complete_ident\tblastrule_complete_wp_coverage\tblastrule_complete_br_coverage\tblastrule_partial_ident\tblastrule_partial_wp_coverage\tblastrule_partial_br_coverage\treportable\ttype\tsubtype\tclass\tsubclass\tfamily_name\n-ACID\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tACID\t\t\t\n-ALL\t\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\t\t\t\t\t\n-AME\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\n-AMR\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n-BIOCIDE\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tBIOCIDE\t\t\t\n-BcII\tbla-B1\tbla2\tNF033095.1\t500.00\t500.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tCARBAPENEM\tBcII family subclass B1 metallo-beta-lactamase\n-CDF_efflux\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\n-CMY2-MIR-ACT-EC\tbla-C\tampC\tNF012173.1\t680.00\t680.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tCMY2/MIR/ACT/EC family class C beta-lactamase\n-EFFLUX\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tefflux\n-HARLDQ_not_B3\tbla-B3\t-\tNF000405.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tHARLDQ motif MBL-fold protein\n-HEAT\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tHEAT\t\t\t\n-HTH_5\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\n-LHR_hdeD\tHEAT\thdeD-GI\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\n-LHR_hsp20A\tHEAT\thsp20\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\n-LHR_hsp20B\tHEAT\tshsP\t-\t0.00\t0.00\t93.00\t90.00\t90.00\t94.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\n-LHR_kefB\tHEAT\tkefB-GI\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\n-LHR_psiE\tHEAT\tpsi-GI\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\n-LHR_trx\tHEAT\ttrxLHR\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\n-LHR_yfdX1\tHEAT\tyfdX1\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\n-LHR_yfdX2\tHEAT\tyfdX2\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\n-MATE_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\n-METAL-RND-IM\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\n-METAL\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tMetal Resistance\n-MFS_efflux_CHL\tMFS_efflux\tcml\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\n-MFS_efflux_qac\tBIOCIDE\tqac\tNF000089.1\t900.00\t900.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQacA/B family quaternary ammonium compound efflux MFS transporter\n-MFS_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\n-MerP_Gneg\tmerP\tmerP\tTIGR02052.1\t92.55\t92.55\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tMETAL\tMERCURY\tMERCURY\tmercury resistance system periplasmic binding protein MerP\n-OM_sidero\tVIRULENCE_Ecoli\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\n-P-type_ATPase\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\n-PERI-SENSOR\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\n-RESPONSE_REG\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tDNA-binding response regulator\n-RND-IM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux RND transporter permease subunit\n-RND-OM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug'..b'ferase Vat(A)\n-vat(B)\tvat\tvat(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(B)\n-vat(C)\tvat\tvat(C)\tNF000097.1\t425.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(C)\n-vat(D)\tvat\tvat(D)\tNF000111.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(D)\n-vat(E)\tvat\tvat(E)\tNF000020.1\t450.00\t450.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(E)\n-vat(F)\tvat\tvat(F)\tNF000147.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(F)\n-vat(H)\tvat\tvat(H)\tNF000504.1\t475.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(H)\n-vat(I)\tvat\tvatI\tNF033468.1\t415.00\t415.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(I)\n-vat\tAMR\tvat\tNF000311.1\t300.00\t300.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tVat family streptogramin A O-acetyltransferase\n-vga(A)\tvga\tvga(A)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(A)\n-vga(B)\tvga\tvga(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(B)\n-vga(C)\tvga\tvga(C)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(C)\n-vga(D)\tvga\tvga(D)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(D)\n-vga(E)\tvga\tvga(E)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(E)\n-vga\tabc-f\tvga\tNF000170.1\t800.00\t800.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tVga family ABC-F type ribosomal protection protein\n-vgb(A)\tvgb\tvgb(A)\tNF000022.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(A)\n-vgb(B)\tvgb\tvgb(B)\tNF000096.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(B)\n-vgb(C)\tvgb\tvgbC\t-\t0.00\t0.00\t84.00\t90.00\t90.00\t88.00\t90.00\t25.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(C)\n-vgb\tAMR\tvgb\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase\n-virF\tVIRULENCE_Ecoli\tvirF\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tAraC family invasion system transcriptional regulator VirF\n-vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tMACROLIDE/PLEUROMUTILIN\tLINCOSAMIDE/STREPTOGRAMIN/TIAMULIN\tABC-F type ribosomal protection protein VmlR\n-vph\tAMR\tvph\tNF000088.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tTUBERACTINOMYCIN\tVIOMYCIN\tviomycin phosphotransferase\n-ybtP\tVIRULENCE\tybtP\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtP\n-ybtQ\tVIRULENCE\tybtQ\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtQ\n-yfeA\tVIRULENCE\tyfeA\t-\t0.00\t0.00\t83.00\t90.00\t90.00\t88.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter substrate-binding protein YfeA\n-yfeB\tVIRULENCE\tyfeB\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter ATP-binding protein YfeB\n-yfeD\tVIRULENCE\tyfeD\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t92.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter permease subunit YfeD\n-zbmA\tble\tzbmA\tNF000479.1\t280.00\t280.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBLEOMYCIN\tZORBAMYCIN\tzorbamycin binding protein ZbmA\n' |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#taxgroup gpipe_taxgroup number_of_nucl_ref_genes -Acinetobacter_baumannii Acinetobacter 0 |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 test-data/test-db/amrfinderplus-db/2021-09-30.1/version.txt --- a/test-data/test-db/amrfinderplus-db/2021-09-30.1/version.txt Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -2021-09-30.1 |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 test-data/test_database.loc --- a/test-data/test_database.loc Fri Sep 16 13:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -# Tab separated with 4 columns: -# - value (Galaxy records this in the Galaxy DB) -# - name (Galaxy shows this in the UI) -# - path (folder name containing the NCBI DB) -test-db-bakta "Database test" ${__HERE__}/test-db |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 tool-data/amrfinderplus_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/amrfinderplus_database.loc.sample Wed Dec 21 20:59:54 2022 +0000 |
| b |
| @@ -0,0 +1,11 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, path +# +# for example +2022-11-10_15:48 2022-10-11.2 ${__HERE__} +amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 /tmp/tmp3as7lw95/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.10_2022-10-11.2 +amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 /tmp/tmp3as7lw95/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.6_2020-03-20.1 +amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 /tmp/tmpqjc1v8il/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.10_2022-10-11.2 +amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 /tmp/tmpqjc1v8il/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.6_2020-03-20.1 |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 tool-data/bakta_database.loc.sample --- a/tool-data/bakta_database.loc.sample Fri Sep 16 13:42:15 2022 +0000 +++ b/tool-data/bakta_database.loc.sample Wed Dec 21 20:59:54 2022 +0000 |
| b |
| @@ -1,3 +1,3 @@ #This is a sample file distributed with Galaxy that enables tools #file has this format (white space characters are TAB characters) -test-db-bakta "Database test" ${__HERE__}/test-db +#V4.0_2022-08-29 7025248 1.5 path/to/db |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Sep 16 13:42:15 2022 +0000 +++ b/tool_data_table_conf.xml.sample Wed Dec 21 20:59:54 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> <table name="bakta_database" comment_char="#"> - <columns>value, name, path</columns> + <columns>value, dbkey, bakta_version, path</columns> <file path="tool-data/bakta_database.loc.sample" /> </table> </tables> |
| b |
| diff -r da5f1924bb2e -r debdc1469b41 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Fri Sep 16 13:42:15 2022 +0000 +++ b/tool_data_table_conf.xml.test Wed Dec 21 20:59:54 2022 +0000 |
| b |
| @@ -1,7 +1,11 @@ <?xml version="1.0"?> <tables> <table name="bakta_database" comment_char="#"> + <columns>value, dbkey, bakta_version, path</columns> + <file path="${__HERE__}/test-data/bakta_database.loc" /> + </table> + <table name="amrfinderplus_database" comment_char="#"> <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/test_database.loc" /> + <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> </table> </tables> |