Mercurial > repos > iuc > tbvcfreport
changeset 0:02d81b994ef5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
| author | iuc |
|---|---|
| date | Thu, 29 Aug 2019 08:18:59 -0400 |
| parents | |
| children | adc0645b945c |
| files | tbvcfreport.xml test-data/rif_resistant.results.json test-data/rif_resistant.vcf test-data/rif_resistant_drug_resistance_report.html test-data/rif_resistant_drug_resistance_report.txt test-data/rif_resistant_variants_report.html test-data/rif_resistant_variants_report.txt |
| diffstat | 7 files changed, 529 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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 @@ +<?xml version="1.0" ?> +<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0"> + <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description> + <macros> + <token name="@TOOL_VERSION@">0.1.7</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + #if $adv.database_uri + export DATABASE_URI='${adv.database_uri}' && + #end if + + #if not '.vcf' in str($input_vcf.element_identifier) + #set $input_vcf_filename = str($input_vcf.element_identifier).replace(' ', '') + '.vcf' + #else + #set $input_vcf_filename = str($input_vcf.element_identifier).replace(' ', '') + #end if + + ln -s '${input_vcf}' '${input_vcf_filename}' && + + #set vcf_name = os.path.splitext(os.path.basename($input_vcf_filename))[0] + + #if $tbprofiler_json + #if not '.json' in str($tbprofiler_json.element_identifier) + #set $tbprofiler_report = str($tbprofiler_json.element_identifier).replace(' ', '') + '.json' + #else + #set $tbprofiler_report = str($tbprofiler_json.element_identifier).replace(' ', '') + #end if + ln -s '${tbprofiler_json}' '${tbprofiler_report}' && + #end if + + tbvcfreport generate + + $filter_udi + + #if $tbprofiler_json + --tbprofiler-report '${tbprofiler_report}' + #end if + + '${input_vcf_filename}' && + + #set variants_report = str(vcf_name) + '_variants_report' + #set html_variants_report = variants_report + '.html' + #set txt_variants_report = variants_report + '.txt' + + mv '${html_variants_report}' '$variants_report_html' && + mv '${txt_variants_report}' '$variants_report_txt' + + #if $tbprofiler_json + #set drug_resistance_report = str(vcf_name) + '_drug_resistance_report' + #set html_drug_resistance_report = drug_resistance_report + '.html' + #set txt_drug_resistance_report = drug_resistance_report + '.txt' + + && mv '${html_drug_resistance_report}' '$drug_resistance_report_html' + && mv '${txt_drug_resistance_report}' '$drug_resistance_report_txt' + #end if + ]]> + </command> + <inputs> + <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" /> + <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" /> + <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" /> + <section name="adv" title="Advanced options" expanded="false"> + <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify on-premise COMBAT-TB-NeoDB URI" help="For people with an on-premise deployment of COMBAT-TB-NeoDB" /> + </section> + </inputs> + <outputs> + <data name="variants_report_html" format="html" label="${tool.name} variants report (html) on ${on_string}" /> + <data name="variants_report_txt" format="txt" label="${tool.name} variants report (text) on ${on_string}" /> + <data name="drug_resistance_report_html" format="html" label="${tool.name} drug resistance report (html) on ${on_string}"> + <filter>tbprofiler_json</filter> + </data> + <data name="drug_resistance_report_txt" format="txt" label="${tool.name} drug resistance report (text) on ${on_string}"> + <filter>tbprofiler_json</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" /> + <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" /> + <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" /> + </test> + <test> + <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" /> + <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" /> + <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" /> + <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" /> + <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" /> + <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" /> + </test> + </tests> + <help> + <![CDATA[ + **tbvcfreport - @TOOL_VERSION@** + + **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB (https://neodb.sanbi.ac.za) + and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/). + + **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report. + + Drug resistance predictions are for **Research Purposes Only** and are produced by TBProfiler (https://github.com/jodyphelan/TBProfiler) + + **Inputs** + + - SnpEff annotated M.tuberculosis VCF file(s) - vcf - **required** + + - TBProfiler Drug Resistance JSON Report - json - **optional** + + **Outputs** + + - Variant Report in HTML and TXT format + + - Drug Resistance Report in HTML and TXT format if provided with a TBProfiler json report + + + **Advanced options**: + + - database_uri - String - Use an on-premise COMBAT-TB-NeoDB (default 'neodb.sanbi.ac.za') - **optional** + + **Further information** + + For more on the **COMBAT-TB Project**, see https://combattb.org. + + For more on **tbvcfreport**, see https://github.com/COMBAT-TB/tbvcfreport. + + For more on **COMBAT-TB-NeoDB**, see https://github.com/COMBAT-TB/combat-tb-neodb. + ]]> + </help> + <citations> + <citation type="bibtex"> +@misc{githubtbvcfreport, + author = {COMBAT-TB}, + year = {2019}, + title = {tbvcfreport}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/COMBAT-TB/tbvcfreport}, +}</citation> + </citations> +</tool>
--- /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
--- /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=<ID=PASS,Description="All filters passed"> +##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=<ID=MT_H37RV_BRD_V5,length=4411532> +##ALT=<ID=*,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> +##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)"> +##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> +##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> +##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> +##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##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
--- /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 @@ +<!DOCTYPE html> +<html> + +<head> + <title></title> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> + <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" rel="stylesheet" + integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous"> + <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"> + <link rel="stylesheet" type="text/css" + href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.bootstrap4.min.css"> + <link rel="stylesheet" type="text/css" + href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.dataTables.min.css"> + </head> + +<body> + <div class="container"> + <div class="row"> + <h2 class="mt-5"> + rif_resistant Report + </h2> + </div> + <div class="row"> + <table class="table table-striped table-hover"> + <caption>Lineage Info</caption> + <thead class="thead-light"> + <tr> + <th scope="col">Species</th> + <th scope="col">Lineage</th> + <th scope="col">Sub-lineage</th> + <th scope="col">Agreement with SNPs from this lineage</th> + </tr> + </thead> + <tbody> + <tr> + <td>M. tuberculosis</td> + <td>Lineage 4</td> + <td> + Not Available + </td> + <td>99%</td> + </tr> + </tbody> + </table> + </div> + <hr> + <div class="row"> + <h3 class="mb-2"> + <a class="text-body" href="https://github.com/jodyphelan/TBProfiler" target="_blank" + rel="noreferrer noopener">TBProfiler</a> + Drug Resistance Report + </h3> +</div> +<div class="row"> + <table id="drug_resistance" class="table table-hover table-bordered table-striped table-sm" cellspacing="0"> + <caption class="mb-3 text-info"> + <strong>Disclaimer</strong>: + Drug resistance predictions are for <strong>Research Purposes Only</strong> and are produced by + <a class="text-info" href="https://github.com/jodyphelan/TBProfiler" target="_blank" + rel="noreferrer noopener">TBProfiler</a>. + </caption> + <thead class="thead-light"> + <tr> + <th scope="col">Drug</th> + <th scope="col">Resistance</th> + <th scope="col">Supporting Mutations</th> + </tr> + </thead> + <tr> + <td>Isoniazid</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Rifampicin</td> + <td>R</td> + <td> <a target="_blank" href="https://explorer.sanbi.ac.za/gene?q=rpoB" + rel="noreferrer noopener">rpoB</a> + (1.0 p.Asp435Val) + </td> + </tr> + <tr> + <td>Ethambutol</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Pyrazinamide</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Streptomycin</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Ethionamide</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Fluoroquinolones</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Amikacin</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Capreomycin</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Kanamycin</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Para-aminosalicylic acid</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Linezolid</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Cycloserine</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Delaminid</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Clofazimine</td> + <td>S</td> + <td></td> + </tr> + <tr> + <td>Bedaquiline</td> + <td>S</td> + <td></td> + </tr> + </table> +</div> + <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" + integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"> + </script> + <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" + integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"> + </script> + <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" + integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"> + </script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/dataTables.buttons.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.bootstrap4.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.flash.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.html5.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.print.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.colVis.min.js"></script> + <script type="text/javascript" language="javascript" class="init"> + $(function () { + var table = $('#vcfreport').DataTable({ + lengthChange: false, + buttons: [{ + extend: 'csv', + text: 'Download CSV', + filename: 'rif_resistant' + }] + }); + table.buttons().container().appendTo('#vcfreport_wrapper .col-md-6:eq(0)'); + }); + </script> + </div> +</body> + +</html> \ No newline at end of file
--- /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.
--- /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 @@ +<!DOCTYPE html> +<html> + +<head> + <title></title> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> + <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" rel="stylesheet" + integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous"> + <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"> + <link rel="stylesheet" type="text/css" + href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.bootstrap4.min.css"> + <link rel="stylesheet" type="text/css" + href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.dataTables.min.css"> + </head> + +<body> + <div class="container"> + <div class="row"> + <h2 class="mt-5"> + rif_resistant Report + </h2> + </div> + <div class="row"> + <table class="table table-striped table-hover"> + <caption>Lineage Info</caption> + <thead class="thead-light"> + <tr> + <th scope="col">Species</th> + <th scope="col">Lineage</th> + <th scope="col">Sub-lineage</th> + <th scope="col">Agreement with SNPs from this lineage</th> + </tr> + </thead> + <tbody> + <tr> + <td>M. tuberculosis</td> + <td>Lineage 4</td> + <td> + Not Available + </td> + <td>99%</td> + </tr> + </tbody> + </table> + </div> + <hr> + <div> + <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html" + target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p> + <p>Kindly check if the '<strong>ANN</strong>' field is present.</p> +</div> + <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" + integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"> + </script> + <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" + integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"> + </script> + <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" + integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"> + </script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/dataTables.buttons.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.bootstrap4.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.flash.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.html5.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.print.min.js"></script> + <script type="text/javascript" charset="utf8" + src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.colVis.min.js"></script> + <script type="text/javascript" language="javascript" class="init"> + $(function () { + var table = $('#vcfreport').DataTable({ + lengthChange: false, + buttons: [{ + extend: 'csv', + text: 'Download CSV', + filename: 'rif_resistant' + }] + }); + table.buttons().container().appendTo('#vcfreport_wrapper .col-md-6:eq(0)'); + }); + </script> + </div> +</body> + +</html> \ No newline at end of file
--- /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