| Previous changeset 0:bae2bc0f1b66 (2024-08-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit 4de98d11ef4e46d92c545f665499be8fd714bac5 |
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modified:
argnorm.xml test-data/blastout.filtered.argnorm.tsv test-data/deeparg_hamronize_argnorm_results.tsv test-data/groot-resfinder-results.tsv |
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| diff -r bae2bc0f1b66 -r d8e95a03321a argnorm.xml --- a/argnorm.xml Wed Aug 28 20:27:17 2024 +0000 +++ b/argnorm.xml Wed Apr 23 09:04:24 2025 +0000 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05"> +<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description> <macros> - <token name="@VERSION@">0.6.0</token> + <token name="@VERSION@">1.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <xrefs> <xref type="bio.tools">argnorm</xref> @@ -11,37 +12,60 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ argnorm - '$tool' + '$choose_tool.tool' + #if $choose_tool.tool == "abricate" or $choose_tool.tool == "groot" --db '$db' + #end if -i '$input' -o '$output' + #if $choose_tool.tool == "hamronization" $hamronized + #end if ]]></command> <inputs> <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" /> - <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" > - <option value="deeparg" selected="true">DeepARG</option> - <option value="argsoap">ARGs_OAP</option> - <option value="abricate">ABRicate</option> - <option value="resfinder">ResFinder</option> - <option value="amrfinderplus">AMRFinderPlus</option> - <option value="groot">Groot</option> - </param> - <param type="select" argument="--db" label="The database you used to do ARG annotation"> - <option value="sarg" selected="true">SARG</option> - <option value="ncbi">NCBI</option> - <option value="resfinder">ResFinder</option> - <option value="deeparg" selected="true">DeepARG</option> - <option value="amrfinderplus">AMRFinderPlus</option> - <option value="megares">MEGARes</option> - <option value="argannot">ARG-ANNOT</option> - <option value="groot-resfinder">Groot ResFinder database </option> - <option value="groot-argannot">Groot ARG-ANNOT database </option> - <option value="groot-card">Groot CARD database </option> - <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option> - <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option> - </param> - <param name="hamronized" type="boolean" label="If the input is hamronized" truevalue="--hamronized" falsevalue="" optional="true" help="Use this if the input is hamronized (processed using the hAMRonization tool)" /> + <conditional name="choose_tool"> + <param type="select" name="tool" label="The tool used to do ARG annotation" help="" > + <option value="deeparg" selected="true">DeepARG</option> + <option value="argsoap">ARGs-OAP</option> + <option value="abricate">ABRicate</option> + <option value="resfinder">ResFinder</option> + <option value="amrfinderplus">AMRFinderPlus</option> + <option value="groot">Groot</option> + <option value="hamronization">hAMRonization</option> + </param> + <when value="deeparg"> + </when> + <when value="argsoap"> + </when> + <when value="abricate"> + <param type="select" argument="--db" label="The database you used to do ARG annotation"> + <option value="sarg" selected="true">SARG</option> + <option value="ncbi">NCBI</option> + <option value="resfinder">ResFinder</option> + <option value="resfinderfg">ResFinder FG</option> + <option value="deeparg" selected="true">DeepARG</option> + <option value="megares">MEGARes</option> + <option value="argannot">ARG-ANNOT</option> + </param> + </when> + <when value="resfinder"> + </when> + <when value="amrfinderplus"> + </when> + <when value="groot"> + <param type="select" argument="--db" label="The database you used to do ARG annotation"> + <option value="groot-resfinder">Groot ResFinder database </option> + <option value="groot-argannot">Groot ARG-ANNOT database </option> + <option value="groot-card">Groot CARD database </option> + <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option> + <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option> + </param> + </when> + <when value="hamronization"> + <param name="hamronized" type="boolean" label="Skip rows with unsupported tools" truevalue="--hamronization_skip_unsupported_tool" falsevalue="" checked="false" help="Combined hAMRonization results can have ARGs detected by unsupported tools (e.g. staramr), --hamronization_skip_unsupported_tool allows to skip rows with unsupported tools"/> + </when> + </conditional> </inputs> <outputs> <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" /> @@ -50,23 +74,27 @@ <!-- Test 1 : input : tsv, output : tsv, tool : groot --> <test> <param name="input" value="resfinder_PSM7J199_R2.report"/> - <param name="tool" value="groot"/> - <param name="db" value="groot-resfinder"/> + <conditional name="choose_tool"> + <param name="tool" value="groot"/> + <param name="db" value="groot-resfinder"/> + </conditional> <output name="output" file="groot-resfinder-results.tsv"/> </test> <!-- Test 2 : input : txt, output : tsv, tool : argsoap --> <test> <param name="input" value="blastout.filtered.txt"/> - <param name="tool" value="argsoap"/> - <param name="db" value="sarg"/> + <conditional name="choose_tool"> + <param name="tool" value="argsoap"/> + </conditional> <output name="output" file="blastout.filtered.argnorm.tsv"/> </test> - <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true --> + <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize --> <test> <param name="input" value="deeparg_hamronize.tsv"/> - <param name="tool" value="deeparg"/> - <param name="db" value="deeparg"/> - <param name="hamronized" value="true"/> + <conditional name="choose_tool"> + <param name="tool" value="hamronization"/> + <param name="hamronized" value="true"/> + </conditional> <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/> </test> </tests> |
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| diff -r bae2bc0f1b66 -r d8e95a03321a test-data/blastout.filtered.argnorm.tsv --- a/test-data/blastout.filtered.argnorm.tsv Wed Aug 28 20:27:17 2024 +0000 +++ b/test-data/blastout.filtered.argnorm.tsv Wed Apr 23 09:04:24 2025 +0000 |
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| b'@@ -1,101 +1,102 @@\n-0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\tARO\tconfers_resistance_to\tresistance_to_drug_classes\n-qseqid\tsseqid\tpident\tlength\tqlen\tslen\tevalue\tbitscore\tqcov\tsample\tscov\tgene\tsubtype\ttype\tcount\tcopy\trpk\trpksum\t\t\t\n-HSM7J4M8@HSM7J4M8_R1@10007@CAVL1ANXX170419:8:1312:3147:65962/1\tgi|751930065|ref|WP_041144773.1|\t84.848\t33\t101\t648\t6.19e-12\t55.5\t0.32673267326732675\tHSM7J4M8\t0.05092592592592592\tgi|751930065|ref|WP_041144773.1|\tmacrolide-lincosamide-streptogramin__macB\tmacrolide-lincosamide-streptogramin\t0.3333333333333333\t0.016975308641975308\t0.51440329218107\t28361.83513176316\tARO:3000535\t\t\n-HSM7J4M8@HSM7J4M8_R1@10017@CAVL1ANXX170419:8:1312:6960:13504/1\tgb|ADP36409.1|ARO:3003730|Bifidobacteria\t100.0\t33\t101\t1107\t9.96e-19\t74.7\t0.32673267326732675\tHSM7J4M8\t0.02981029810298103\tgb|ADP36409.1|ARO:3003730|Bifidobacteria\tmupirocin__Bifidobacteria intrinsic ileS conferring resistance to mupirocin\tmupirocin\t1.0\t0.02981029810298103\t0.903342366757001\t28361.83513176316\tARO:3003730\tARO:3000554\tARO:3007151\n-HSM7J4M8@HSM7J4M8_R1@10018@CAVL1ANXX170419:8:1312:7015:67833/1\tgi|490355791|ref|WP_004235564.1|\t87.5\t32\t101\t510\t4.28e-13\t58.9\t0.31683168316831684\tHSM7J4M8\t0.06274509803921569\tgi|490355791|ref|WP_004235564.1|\tmultidrug__emrB\tmultidrug\t0.3333333333333333\t0.02091503267973856\t0.65359477124183\t28361.83513176316\tARO:3004597\tARO:0000032\tARO:3000007\n-HSM7J4M8@HSM7J4M8_R1@10019@CAVL1ANXX170419:8:1312:7329:85173/1\tgb|AAF74725.1|ARO:3004659|Mef(En2)\t100.0\t33\t101\t401\t1.8e-16\t68.2\t0.32673267326732675\tHSM7J4M8\t0.08229426433915212\tgb|AAF74725.1|ARO:3004659|Mef(En2)\tmacrolide-lincosamide-streptogramin__mef(En2)\tmacrolide-lincosamide-streptogramin\t1.0\t0.08229426433915212\t2.4937655860349124\t28361.83513176316\tARO:3004659\tARO:0000046\tARO:0000017\n-HSM7J4M8@HSM7J4M8_R1@10023@CAVL1ANXX170419:8:1312:8170:40475/1\tZP_04557016\t100.0\t33\t101\t657\t2.5e-16\t67.8\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tZP_04557016\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8@HSM7J4M8_R1@10028@CAVL1ANXX170419:8:1312:8966:29123/1\tZP_04557016\t96.97\t33\t101\t657\t1.36e-17\t71.6\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tZP_04557016\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8@HSM7J4M8_R1@1002@CAVL1ANXX170419:7:1115:3411:87969/1\tgb|AEY83581|ARO:3000510|mupB\t84.848\t33\t101\t1033\t6.34e-16\t66.6\t0.32673267326732675\tHSM7J4M8\t0.031945788964181994\tgb|AEY83581|ARO:3000510|mupB\tmupirocin__mupB\tmupirocin\t1.0\t0.031945788964181994\t0.9680542110358181\t28361.83513176316\tARO:3000510\tARO:3000554\tARO:3007151\n-HSM7J4M8@HSM7J4M8_R1@10033@CAVL1ANXX170419:8:1312:9879:14531/1\tgi|511019447|ref|WP_016273783.1|\t100.0\t33\t101\t296\t2.91e-18\t72.8\t0.32673267326732675\tHSM7J4M8\t0.11148648648648649\tgi|511019447|ref|WP_016273783.1|\tbeta_lactam__CblA-1\tbeta_lactam\t1.0\t0.11148648648648649\t3.3783783783783785\t28361.83513176316\tARO:3002999\tARO:0000032,ARO:3004129\tARO:3000007,ARO:3000007\n-HSM7J4M8@HSM7J4M8_R1@10034@CAVL1ANXX170419:8:1312:9988:52653/1\tACI02041\t100.0\t33\t101\t639\t3.53e-17\t70.5\t0.32673267326732675\tHSM7J4M8\t0.051643192488262914\tACI02041\ttetracycline__tet(W)\ttetracycline\t1.0\t0.051643192488262914\t1.5649452269170578\t28361.83513176316\tARO:3000194\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8@HSM7J4M8_R1@10036@CAVL1ANXX170419:8:1313:10501:70436/1\tP70882\t100.0\t28\t85\t641\t5.38e-12\t55.5\t0.32941176470588235\tHSM7J4M8\t0.0436817472698908\tP70882\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0436817472698908\t1.5600624024960998\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:300052'..b'000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\terythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\tmacrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic\n+HSM7J4M8@HSM7J4M8_R1@10552@CAVL1ANXX170419:8:2103:4941:41693/1\tP70882\t100.0\t33\t101\t641\t2.21e-18\t73.9\t0.32673267326732675\tHSM7J4M8\t0.0514820592823713\tP70882\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0514820592823713\t1.5600624024960998\t28361.83513176316\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8@HSM7J4M8_R1@10556@CAVL1ANXX170419:8:2103:6322:54059/1\tAAM48125\t100.0\t33\t101\t321\t5.77e-17\t69.3\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48125\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\tARO:3003002\tCfxA2\tStrict\tARO:3009106\tsecond-generation cephalosporin\tARO:3000007\tbeta-lactam antibiotic\n+HSM7J4M8@HSM7J4M8_R1@10568@CAVL1ANXX170419:8:2103:9384:19852/1\tBAD46890\t100.0\t33\t101\t657\t2.63e-17\t70.9\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tBAD46890\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8@HSM7J4M8_R1@10569@CAVL1ANXX170419:8:2103:9417:90711/1\tAAZ79478\t100.0\t33\t101\t657\t2.68e-16\t67.8\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tAAZ79478\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8@HSM7J4M8_R1@10570@CAVL1ANXX170419:8:2103:9525:62852/1\tAAM48116\t100.0\t33\t101\t321\t2.25e-17\t70.5\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48116\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\tARO:3003002\tCfxA2\tStrict\tARO:3009106\tsecond-generation cephalosporin\tARO:3000007\tbeta-lactam antibiotic\n' |
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| diff -r bae2bc0f1b66 -r d8e95a03321a test-data/deeparg_hamronize_argnorm_results.tsv --- a/test-data/deeparg_hamronize_argnorm_results.tsv Wed Aug 28 20:27:17 2024 +0000 +++ b/test-data/deeparg_hamronize_argnorm_results.tsv Wed Apr 23 09:04:24 2025 +0000 |
| b |
| b'@@ -1,100 +1,101 @@\n-input_file_name\tgene_symbol\tgene_name\treference_database_name\treference_database_version\treference_accession\tanalysis_software_name\tanalysis_software_version\tgenetic_variation_type\tantimicrobial_agent\tcoverage_percentage\tcoverage_depth\tcoverage_ratio\tdrug_class\tinput_gene_length\tinput_gene_start\tinput_gene_stop\tinput_protein_length\tinput_protein_start\tinput_protein_stop\tinput_sequence_id\tnucleotide_mutation\tnucleotide_mutation_interpretation\tpredicted_phenotype\tpredicted_phenotype_confidence_level\tamino_acid_mutation\tamino_acid_mutation_interpretation\treference_gene_length\treference_gene_start\treference_gene_stop\treference_protein_length\treference_protein_start\treference_protein_stop\tresistance_mechanism\tstrand_orientation\tsequence_identity\tARO\tconfers_resistance_to\tresistance_to_drug_classes\n-HSM7J4M8\tTETQ\tZP_04557016|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZP_04557016\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t191\t223\t\t\t\tCAVL1ANXX170419:8:1211:20929:16342/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t274\t306\t\t\t\tCAVL1ANXX170419:8:1211:20929:16342/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8\tUGD\tAAC75089.1|FEATURES|ugd|peptide|ugd\tdeeparg_db\t1\tAAC75089.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tpeptide\t\t242\t274\t\t\t\tCAW05ANXX170413:3:1311:9080:27889/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\tARO:3003577\tARO:3000454\tARO:3000053\n-HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t452\t484\t\t\t\tCAVL1ANXX170419:7:1112:17911:9537/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n-HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t428\t471\t\t\t\tCAW05ANXX170413:3:2313:9964:68847/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t81.8\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n-HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t245\t277\t\t\t\tCAW05ANXX170413:4:2211:15535:39005/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t125\t156\t\t\t\tCAW05ANXX170413:3:1315:16625:39188/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n-HSM7J4M8\tCLASS_A\tP30898|FEATURES|class_A|beta-lactam|class_A\tdeeparg_db\t1\tP30898\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tbeta-lactam\t\t168\t214\t\t\t\tCAW05ANXX170413:4:2110:17870:97415/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3002999\tARO:0000032,ARO:3004129\tARO:3000007,ARO:3000007\n-HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1034\t1066\t\t\t\tCAVL1ANXX170419:7:2114:1131:86489/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t84.8\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n-HSM7J4M8\tTETW\tCAO78565|FEATURES|tetW|tetracycline|tetW\tdeeparg_db\t1\tCAO78565\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t395\t435\t\t\t\tCAW05ANXX170413:2:2115:3176:4503/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000194\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3'..b'acycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t97\t129\t\t\t\tCAW05ANXX170413:3:1307:3879:36407/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8\tTETQ\tZ21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZ21523.gene.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t21\t53\t\t\t\tCAW05ANXX170413:3:1307:3879:36407/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\ttet(Q)\tPerfect\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1017\t1049\t\t\t\tCAW05ANXX170413:4:2210:5154:42720/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t93.9\tARO:3000501\trpoB2\tPerfect\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\trifampin,rifaximin,rifabutin,rifapentine\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\trifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic\n+HSM7J4M8\tTETQ\tZP_04557016|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZP_04557016\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t245\t275\t\t\t\tCAW05ANXX170413:4:2109:16067:23574/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t96.8\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t547\t579\t\t\t\tCAVL1ANXX170419:8:1310:19520:23144/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t786\t817\t\t\t\tCAW05ANXX170413:2:2307:7561:79956/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t96.9\tARO:3000501\trpoB2\tPerfect\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\trifampin,rifaximin,rifabutin,rifapentine\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\trifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic\n+HSM7J4M8\tTETQ\tZ21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZ21523.gene.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t489\t521\t\t\t\tCAW05ANXX170413:3:2104:12736:98854/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\ttet(Q)\tPerfect\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n' |
| b |
| diff -r bae2bc0f1b66 -r d8e95a03321a test-data/groot-resfinder-results.tsv --- a/test-data/groot-resfinder-results.tsv Wed Aug 28 20:27:17 2024 +0000 +++ b/test-data/groot-resfinder-results.tsv Wed Apr 23 09:04:24 2025 +0000 |
| b |
| b'@@ -1,29 +1,30 @@\n-0\t1\t2\t3\tARO\tconfers_resistance_to\tresistance_to_drug_classes\n-erm(G)_1_M15332\t70\t735\t240M19D121M99D173M83D\tARO:3000522\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n-erm(B)_15_U48430\t107\t753\t11D287M63D196M22D89M85D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n-erm(B)_6_AF242872\t155\t747\t11D299M51D312M74D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n-erm(B)_21_U35228\t125\t738\t53D163M145D363M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n-erm(B)_10_U86375\t143\t738\t11D205M145D363M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n-erm(B)_11_M19270\t112\t738\t11D205M2D73M70D127M12D224M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n-lnu(C)_1_AY928180\t41\t495\t51D277M14D148M5D\tARO:3002837\tARO:0000046\tARO:0000017\n-erm(B)_2_K00551\t126\t738\t'..b'ic\n+erm(B)_1_JN899585\t163\t738\t11D287M63D363M14D\tARO:3000375\tErmB\tStrict\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\terythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\tmacrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic\n+tet(W)_4_AJ427422\t127\t1920\t3D1900M17D\t\t\t\t\t\t\t\n+erm(B)_12_U18931\t198\t738\t11D713M14D\tARO:3000375\tErmB\tStrict\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\terythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\tmacrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic\n+tet(W)_1_DQ060146\t120\t1920\t3D1018M49D833M17D\tARO:3000194\ttet(W)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n+tet(Q)_1_L33696\t2132\t1926\t1D708M3D334M2D874M4D\tARO:3000191\ttet(Q)\tStrict\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\ttetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\ttetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic\n' |