# HG changeset patch # User iuc # Date 1567081139 14400 # Node ID 02d81b994ef59178df771210961456498d8d05a8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865" diff -r 000000000000 -r 02d81b994ef5 tbvcfreport.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tbvcfreport.xml Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,143 @@ + + + - generate HTML report from SnpEff annotated M.tb VCF(s) + + 0.1.7 + + + tbvcfreport + + + + + + + + +
+ +
+ + + + + + tbprofiler_json + + + tbprofiler_json + + + + + + + + + + + + + + + + + + + + + + +@misc{githubtbvcfreport, + author = {COMBAT-TB}, + year = {2019}, + title = {tbvcfreport}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/COMBAT-TB/tbvcfreport}, +} + + diff -r 000000000000 -r 02d81b994ef5 test-data/rif_resistant.results.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rif_resistant.results.json Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,1 @@ +{"missing_pos": [["Chromosome", 763404], ["Chromosome", 763405], ["Chromosome", 763406], ["Chromosome", 763407], ["Chromosome", 763408], ["Chromosome", 763409], ["Chromosome", 763410], ["Chromosome", 763411], ["Chromosome", 763412], ["Chromosome", 763413], ["Chromosome", 763414], ["Chromosome", 763415], ["Chromosome", 763416], ["Chromosome", 763417], ["Chromosome", 763418], ["Chromosome", 763419], ["Chromosome", 763420], ["Chromosome", 1834082], ["Chromosome", 1834083], ["Chromosome", 1834084], ["Chromosome", 1834085], ["Chromosome", 1834086], ["Chromosome", 1834087], ["Chromosome", 1834088], ["Chromosome", 1834089], ["Chromosome", 1834090], ["Chromosome", 1834091], ["Chromosome", 1834092], ["Chromosome", 1834093], ["Chromosome", 1834094], ["Chromosome", 1834095], ["Chromosome", 1834251], ["Chromosome", 1834252], ["Chromosome", 1834253], ["Chromosome", 1834254], ["Chromosome", 1834255], ["Chromosome", 1834256], ["Chromosome", 1834257], ["Chromosome", 1834258], ["Chromosome", 1834259], ["Chromosome", 1834260], ["Chromosome", 1834261], ["Chromosome", 1834262], ["Chromosome", 1834263], ["Chromosome", 1834264], ["Chromosome", 1834265], ["Chromosome", 1834266], ["Chromosome", 1834267], ["Chromosome", 1834268], ["Chromosome", 1834269], ["Chromosome", 1834270], ["Chromosome", 1834271], ["Chromosome", 1834272], ["Chromosome", 1834273], ["Chromosome", 4245997], ["Chromosome", 4245998], ["Chromosome", 4245999], ["Chromosome", 4246000], ["Chromosome", 4246001], ["Chromosome", 4246002], ["Chromosome", 4246003], ["Chromosome", 4246004], ["Chromosome", 4246005], ["Chromosome", 4246006], ["Chromosome", 4246007], ["Chromosome", 4246008], ["Chromosome", 4246009], ["Chromosome", 4246010], ["Chromosome", 4246011], ["Chromosome", 4246012], ["Chromosome", 4246155], ["Chromosome", 4246156], ["Chromosome", 4246157], ["Chromosome", 4246158], ["Chromosome", 4246159], ["Chromosome", 4246160], ["Chromosome", 4246161], ["Chromosome", 4246162], ["Chromosome", 4246163], ["Chromosome", 4246164], ["Chromosome", 4246165], ["Chromosome", 4246166], ["Chromosome", 4246167], ["Chromosome", 4246168], ["Chromosome", 4246169], ["Chromosome", 4246170], ["Chromosome", 4246171], ["Chromosome", 4246172], ["Chromosome", 4246173], ["Chromosome", 4246174], ["Chromosome", 4246175], ["Chromosome", 4246176], ["Chromosome", 4246177], ["Chromosome", 4246178], ["Chromosome", 4246179], ["Chromosome", 4246180], ["Chromosome", 4246181], ["Chromosome", 4246182], ["Chromosome", 4246183], ["Chromosome", 4246184], ["Chromosome", 4248018], ["Chromosome", 4248019], ["Chromosome", 4248020], ["Chromosome", 4248021], ["Chromosome", 4248022], ["Chromosome", 4248023], ["Chromosome", 4248024], ["Chromosome", 4248025], ["Chromosome", 4248026], ["Chromosome", 4248027], ["Chromosome", 4248028], ["Chromosome", 4248029], ["Chromosome", 4248030], ["Chromosome", 4248031], ["Chromosome", 4248032], ["Chromosome", 4248033], ["Chromosome", 4248034], ["Chromosome", 4248035], ["Chromosome", 4248036], ["Chromosome", 4248037], ["Chromosome", 4248038], ["Chromosome", 4248039], ["Chromosome", 4248040], ["Chromosome", 4248041], ["Chromosome", 4248042], ["Chromosome", 4248043], ["Chromosome", 4248044], ["Chromosome", 4248045], ["Chromosome", 4248046], ["Chromosome", 4248047], ["Chromosome", 4248184], ["Chromosome", 4248185], ["Chromosome", 4248186], ["Chromosome", 4248187], ["Chromosome", 4248188], ["Chromosome", 4248189], ["Chromosome", 4248190], ["Chromosome", 4248191], ["Chromosome", 4248192], ["Chromosome", 4248193], ["Chromosome", 4248194], ["Chromosome", 4248195], ["Chromosome", 4248196], ["Chromosome", 4248197], ["Chromosome", 4248198], ["Chromosome", 4248199], ["Chromosome", 4248200], ["Chromosome", 4248201], ["Chromosome", 4248202], ["Chromosome", 4248203], ["Chromosome", 4248204], ["Chromosome", 4248205], ["Chromosome", 4248206], ["Chromosome", 4248207], ["Chromosome", 4248208], ["Chromosome", 4248209], ["Chromosome", 4248210], ["Chromosome", 4248211], ["Chromosome", 4248212], ["Chromosome", 4248213], ["Chromosome", 4248214], ["Chromosome", 4248215]], "qc": {"pct_reads_mapped": 87.21, "num_reads_mapped": 5515}, "missing_regions": {"Rv0005": 1.0, "Rv0006": 1.0, "Rv0667": 0.0, "Rv0668": 0.9804707060590886, "Rv0678": 1.0, "Rv0682": 1.0, "Rv0701": 1.0, "Rv1267c": 1.0, "rrs": 1.0, "rrl": 1.0, "Rv1483": 1.0, "Rv1484": 1.0, "Rv1630": 0.9029247044181705, "Rv1694": 1.0, "Rv1908c": 1.0, "Rv2043c": 1.0, "Rv2245": 1.0, "Rv2416c": 1.0, "Rv2428": 1.0, "Rv2447c": 1.0, "Rv2671": 1.0, "Rv2754c": 1.0, "Rv2764c": 1.0, "Rv2780": 1.0, "Rv3261": 1.0, "Rv3423c": 1.0, "Rv3601c": 1.0, "Rv3793": 1.0, "Rv3794": 0.9575037147102526, "Rv3795": 0.9584344660194175, "Rv3854c": 1.0, "Rv3855": 1.0, "Rv3919c": 1.0}, "lineage": [{"lin": "lineage2", "family": "East-Asian", "spoligotype": "Beijing", "rd": "RD105", "frac": 1.0}, {"lin": "lineage2.2", "family": "East-Asian (Beijing)", "spoligotype": "Beijing-RD207", "rd": "RD105;RD207", "frac": 1.0}, {"lin": "lineage2.2.2", "family": "East-Asian (Beijing)", "spoligotype": "Beijing-RD105/RD207", "rd": "RD105;RD207", "frac": 1.0}], "main_lin": "lineage2", "sublin": "lineage2.2.2", "dr_variants": [{"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 761110, "type": "missense", "change": "p.Asp435Val", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "435D>435V", "drug": "rifampicin"}], "other_variants": [{"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 763031, "type": "synonymous", "change": "c.3225T>C", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "3225T>C"}, {"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 1834177, "type": "synonymous", "change": "c.636A>C", "freq": 1.0, "locus_tag": "Rv1630", "gene": "rpsA", "_internal_change": "636A>C"}], "XDR": "", "MDR": "", "drtype": "Drug-resistant", "id": "rif_resistant", "tbprofiler_version": "2.1.0", "pipeline": {"mapper": "bwa", "variant_caller": "BCFtools"}} \ No newline at end of file diff -r 000000000000 -r 02d81b994ef5 test-data/rif_resistant.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rif_resistant.vcf Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,53 @@ +##fileformat=VCFv4.2 +##FILTER= +##bcftoolsVersion=1.9+htslib-1.9 +##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam +##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa +##contig= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_callVersion=1.9+htslib-1.9 +##bcftools_callCommand=call --ploidy 1 -c -v rif_resistant.mpileup; Date=Tue Apr 2 06:47:33 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant.bam +MT_H37RV_BRD_V5 15890 . G A 225.007 . DP=58;VDB=0.0163018;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,24;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 154990 . G T 225.007 . DP=57;VDB=0.997362;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,18,38;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 346693 . G T 225.007 . DP=27;VDB=0.365109;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,14,12;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 449194 . G A 225.007 . DP=29;VDB=0.387982;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,5,21;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 497491 . G A 225.007 . DP=78;VDB=0.57291;SGB=-0.693147;MQSB=0.99133;MQ0F=0;AF1=1;AC1=1;DP4=0,0,53,24;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 761110 . A T 225.007 . DP=59;VDB=0.35459;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,32;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 763031 . T C 225.007 . DP=85;VDB=0.401561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,46;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 811753 . C T 225.007 . DP=55;VDB=0.241716;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,27,24;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 1565566 . C T 225.007 . DP=52;VDB=0.650985;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,13,36;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 1833729 . TCCCC TCCCCCC 12.7055 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=1;DP4=0,0,0,1;MQ=54;FQ=-999 GT:PL 1:50,3,0 +MT_H37RV_BRD_V5 1834177 . A C 225.007 . DP=76;VDB=0.880419;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,42,29;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 1849051 . C T 225.007 . DP=86;VDB=0.199205;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,45;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 2505085 . G A 225.007 . DP=48;VDB=0.280048;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,32,13;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 2543395 . T C 225.007 . DP=88;VDB=0.167176;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,37,46;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 2640807 . G A 225.007 . DP=55;VDB=0.218547;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,21;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 2775361 . C T 225.007 . DP=99;VDB=0.0864314;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,46,44;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 2789798 . G T 225.007 . DP=72;VDB=0.231858;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,35;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 3477942 . A G 225.007 . DP=100;VDB=0.912557;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,45,52;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 3587446 . G A 225.007 . DP=59;VDB=0.0078857;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,24;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 4254431 . G A 225.007 . DP=58;VDB=0.120561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,33;MQ=60;FQ=-999 GT:PL 1:255,0 +MT_H37RV_BRD_V5 4254477 . T C 225.007 . DP=30;VDB=0.000342098;SGB=-0.693021;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,10,17;MQ=60;FQ=-999 GT:PL 1:255,0 diff -r 000000000000 -r 02d81b994ef5 test-data/rif_resistant_drug_resistance_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.html Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,202 @@ + + + + + + + + + + + + + + +
+
+

+ rif_resistant Report +

+
+
+ + + + + + + + + + + + + + + + + + +
Lineage Info
SpeciesLineageSub-lineageAgreement with SNPs from this lineage
M. tuberculosisLineage 4 + Not Available + 99%
+
+
+
+

+ TBProfiler + Drug Resistance Report +

+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Disclaimer: + Drug resistance predictions are for Research Purposes Only and are produced by + TBProfiler. +
DrugResistanceSupporting Mutations
IsoniazidS
RifampicinR rpoB + (1.0 p.Asp435Val) +
EthambutolS
PyrazinamideS
StreptomycinS
EthionamideS
FluoroquinolonesS
AmikacinS
CapreomycinS
KanamycinS
Para-aminosalicylic acidS
LinezolidS
CycloserineS
DelaminidS
ClofazimineS
BedaquilineS
+
+ + + + + + + + + + + + + + + +
+ + + \ No newline at end of file diff -r 000000000000 -r 02d81b994ef5 test-data/rif_resistant_drug_resistance_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.txt Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,25 @@ +#Rif_resistant Report +#Species Lineage Sub-lineage Agreement +M. tuberculosis Lineage 4 99% + +#TBProfiler Drug Resistance Report + +#Drug Resistance Supporting Mutations +Isoniazid S +Rifampicin R rpoB(1.0-p.Asp435Val) +Ethambutol S +Pyrazinamide S +Streptomycin S +Ethionamide S +Fluoroquinolones S +Amikacin S +Capreomycin S +Kanamycin S +Para-aminosalicylic acid S +Linezolid S +Cycloserine S +Delaminid S +Clofazimine S +Bedaquiline S + +#Drug resistance predictions are for research purposes only and are produced by the TBProfiler software. diff -r 000000000000 -r 02d81b994ef5 test-data/rif_resistant_variants_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rif_resistant_variants_report.html Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + +
+
+

+ rif_resistant Report +

+
+
+ + + + + + + + + + + + + + + + + + +
Lineage Info
SpeciesLineageSub-lineageAgreement with SNPs from this lineage
M. tuberculosisLineage 4 + Not Available + 99%
+
+
+
+

No variant data was found for this VCF file. Is it a SnpEff annotated VCF file?

+

Kindly check if the 'ANN' field is present.

+
+ + + + + + + + + + + + + + + +
+ + + \ No newline at end of file diff -r 000000000000 -r 02d81b994ef5 test-data/rif_resistant_variants_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rif_resistant_variants_report.txt Thu Aug 29 08:18:59 2019 -0400 @@ -0,0 +1,5 @@ +#Rif_resistant Report +#Species Lineage Sub-lineage Agreement +M. tuberculosis Lineage 4 99% + +#CHR GENE IDENTIFIER PRODUCT TYPE ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHAWAY