Mercurial > repos > blankenberg > naive_variant_caller
changeset 16:07e71cf6c8ef draft
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
| author | blankenberg |
|---|---|
| date | Tue, 03 Apr 2018 10:52:11 -0400 |
| parents | aff38ea879f1 |
| children | 6be51647d31a |
| files | naive_variant_caller.xml test-data/fake_phiX174_reads_1_test_out_1.vcf test-data/fake_phiX174_reads_1_test_out_2.vcf |
| diffstat | 3 files changed, 114 insertions(+), 44 deletions(-) [+] |
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--- a/naive_variant_caller.xml Wed Feb 28 16:01:52 2018 -0500 +++ b/naive_variant_caller.xml Tue Apr 03 10:52:11 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3"> +<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.4"> <description> - tabulate variable sites from BAM datasets</description> <requirements> - <requirement type="package" version="0.0.3">nvc</requirement> + <requirement type="package" version="0.0.4">nvc</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -103,7 +103,7 @@ <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/> - <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/> + <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="True" label="Report counts by strand"/> <conditional name="advanced_options"> <param name="advanced_options_selector" type="select" label="Show Advanced Options"> @@ -145,6 +145,21 @@ <param name="coverage_dtype" value="uint8" /> <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" /> </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" /> + <param name="ref_file" value="phiX174.fasta" ftype="fasta" /> + <param name="regions" value="0" /> + <param name="min_support_depth" value="0" /> + <param name="min_base_quality" value="" /> + <param name="min_mapping_quality" value="" /> + <param name="ploidy" value="2" /> + <param name="variants_only" value="False" /> + <param name="use_strand" value="True" /> + <param name="advanced_options_selector" value="advanced" /> + <param name="coverage_dtype" value="uint8" /> + <output name="output_vcf" file="fake_phiX174_reads_1_test_out_2.vcf" compare="contains" /> + </test> </tests> <help> The **Naive Variant Caller** tool (NVC).
--- a/test-data/fake_phiX174_reads_1_test_out_1.vcf Wed Feb 28 16:01:52 2018 -0500 +++ b/test-data/fake_phiX174_reads_1_test_out_1.vcf Tue Apr 03 10:52:11 2018 -0400 @@ -1,4 +1,5 @@ -##fileformat=VCFv4.1 +##fileformat=VCFv4.3 +##source=Naive Variant Caller version 0.0.4 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> @@ -6,46 +7,46 @@ ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1411 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=1, -phiX174 1412 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=3, -phiX174 1413 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=5, -phiX174 1414 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=6, -phiX174 1415 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=7, -phiX174 1416 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=8, -phiX174 1417 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=9, -phiX174 1418 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, -phiX174 1419 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1420 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1421 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, -phiX174 1422 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, -phiX174 1423 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, +phiX174 1411 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=1, +phiX174 1412 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=3, +phiX174 1413 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=5, +phiX174 1414 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=6, +phiX174 1415 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=7, +phiX174 1416 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=8, +phiX174 1417 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=9, +phiX174 1418 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10, +phiX174 1419 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1420 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1421 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10, +phiX174 1422 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10, +phiX174 1423 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, phiX174 1424 . C A . . AC=7;AF=0.7 GT:AC:AF:NC 1/0:7:0.7:A=7,C=3, -phiX174 1425 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1426 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, -phiX174 1427 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1428 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, -phiX174 1429 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1430 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1431 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1432 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, -phiX174 1433 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, -phiX174 1434 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1435 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1436 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1437 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, -phiX174 1438 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1439 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, -phiX174 1440 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1441 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, -phiX174 1442 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, -phiX174 1443 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, -phiX174 1444 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, -phiX174 1445 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, +phiX174 1425 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1426 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10, +phiX174 1427 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1428 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10, +phiX174 1429 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1430 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1431 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1432 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10, +phiX174 1433 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10, +phiX174 1434 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1435 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1436 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1437 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10, +phiX174 1438 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1439 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10, +phiX174 1440 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1441 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10, +phiX174 1442 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10, +phiX174 1443 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10, +phiX174 1444 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, +phiX174 1445 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10, phiX174 1446 . C T . . AC=3;AF=0.3 GT:AC:AF:NC 0/1:3:0.3:C=7,T=3, phiX174 1447 . T A . . AC=2;AF=0.222222222222 GT:AC:AF:NC 0/0:2:0.222222222222:A=2,T=7, -phiX174 1448 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=7, -phiX174 1449 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=5, -phiX174 1450 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=4, -phiX174 1451 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=3, -phiX174 1452 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=2, -phiX174 1453 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=1, +phiX174 1448 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=7, +phiX174 1449 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=5, +phiX174 1450 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=4, +phiX174 1451 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=3, +phiX174 1452 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=2, +phiX174 1453 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=1,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_phiX174_reads_1_test_out_2.vcf Tue Apr 03 10:52:11 2018 -0400 @@ -0,0 +1,54 @@ +##fileformat=VCFv4.3 +##source=Naive Variant Caller version 0.0.4 +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> +##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample +phiX174 1411 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=1, +phiX174 1412 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=3, +phiX174 1413 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=5, +phiX174 1414 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=6, +phiX174 1415 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=7, +phiX174 1416 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=8, +phiX174 1417 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=9, +phiX174 1418 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, +phiX174 1419 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1420 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1421 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, +phiX174 1422 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, +phiX174 1423 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1424 . C A . . AC=7;AF=0.7;SB=+Inf GT:AC:AF:SB:NC 1/0:7:0.7:+Inf:+A=7,+C=3, +phiX174 1425 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1426 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, +phiX174 1427 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1428 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, +phiX174 1429 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1430 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1431 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1432 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, +phiX174 1433 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, +phiX174 1434 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1435 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1436 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1437 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, +phiX174 1438 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1439 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, +phiX174 1440 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1441 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, +phiX174 1442 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, +phiX174 1443 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, +phiX174 1444 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1445 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, +phiX174 1446 . C T . . AC=3;AF=0.3;SB=+Inf GT:AC:AF:SB:NC 0/1:3:0.3:+Inf:+C=7,+T=3, +phiX174 1447 . T A . . AC=2;AF=0.222222222222;SB=+Inf GT:AC:AF:SB:NC 0/0:2:0.222222222222:+Inf:+A=2,+T=7, +phiX174 1448 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=7, +phiX174 1449 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=5, +phiX174 1450 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=4, +phiX174 1451 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=3, +phiX174 1452 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=2, +phiX174 1453 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=1,