Mercurial > repos > artbio > lumpy_smoove
changeset 8:b4dec06d8fc6 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
| author | artbio |
|---|---|
| date | Sun, 09 May 2021 17:09:33 +0000 |
| parents | 8b0005fdfd04 |
| children | 7dcf61950215 |
| files | lumpy_smoove.xml test-data/result-1.vcf test-data/result-2.vcf test-data/result-3.vcf test-data/result-4.vcf test-data/result-5.vcf test-data/result-6.vcf vcf2hrdetect.xml |
| diffstat | 8 files changed, 25 insertions(+), 22 deletions(-) [+] |
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--- a/lumpy_smoove.xml Sun Apr 18 17:08:22 2021 +0000 +++ b/lumpy_smoove.xml Sun May 09 17:09:33 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy7"> +<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy8"> <description>find structural variants using the smoove workflow</description> <macros> <import>macro_lumpy_smoove.xml</import>
--- a/test-data/result-1.vcf Sun Apr 18 17:08:22 2021 +0000 +++ b/test-data/result-1.vcf Sun May 09 17:09:33 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20200826 +##fileDate=20210508 ##reference=reference.fa ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> @@ -46,14 +46,14 @@ ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> ##contig=<ID=chrI,length=15072434> ##smoove_version=0.2.5 +##smoove_count_stats=celegans-1:2869,2691,194,304 ##smoove_count_stats=celegans-2:2531,2421,134,276 -##smoove_count_stats=celegans-1:2869,2691,194,304 ##source=LUMPY ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:53:42 2020 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:20:12 2021 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 -##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:53:42 2020 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:20:12 2021 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 chrI 10416569 1 N <DUP> 170.7 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69 1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
--- a/test-data/result-2.vcf Sun Apr 18 17:08:22 2021 +0000 +++ b/test-data/result-2.vcf Sun May 09 17:09:33 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20200826 +##fileDate=20210508 ##reference=reference.fa ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> @@ -50,10 +50,10 @@ ##smoove_count_stats=celegans-1:2869,2691,202,330 ##source=LUMPY ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:54:42 2020 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:20:59 2021 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 -##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:54:42 2020 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:20:59 2021 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 chrI 10416569 1 N <DUP> 170.7 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69 1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
--- a/test-data/result-3.vcf Sun Apr 18 17:08:22 2021 +0000 +++ b/test-data/result-3.vcf Sun May 09 17:09:33 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20200826 +##fileDate=20210508 ##reference=reference.fa ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> @@ -50,10 +50,10 @@ ##smoove_count_stats=celegans-1:2869,2691,202,330 ##source=LUMPY ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:55:52 2020 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:21:48 2021 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 -##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:55:52 2020 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:21:48 2021 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-2 celegans-1 chrI 10416569 1 N <DUP> 170.7 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69
--- a/test-data/result-4.vcf Sun Apr 18 17:08:22 2021 +0000 +++ b/test-data/result-4.vcf Sun May 09 17:09:33 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20200826 +##fileDate=20210508 ##reference=reference.fa ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> @@ -48,12 +48,12 @@ ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> ##contig=<ID=chrI,length=15072434> ##smoove_version=0.2.5 +##smoove_count_stats=celegans-2:2531,2421,156,296 ##smoove_count_stats=celegans-1:2869,2691,202,330 -##smoove_count_stats=celegans-2:2531,2421,156,296 ##source=LUMPY ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 -##bcftools_viewCommand=view -O z -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:57:03 2020 +##bcftools_viewCommand=view -O z -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:22:36 2021 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 chrI 10416569 1 N <DUP> 170.7 . 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GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69 1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
--- a/test-data/result-5.vcf Sun Apr 18 17:08:22 2021 +0000 +++ b/test-data/result-5.vcf Sun May 09 17:09:33 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20200827 +##fileDate=20210508 ##reference=reference.fa ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> @@ -49,10 +49,10 @@ ##smoove_count_stats=celegans-1:2869,2691,202,330 ##source=LUMPY ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Thu Aug 27 18:59:21 2020 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:23:15 2021 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 -##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Thu Aug 27 18:59:21 2020 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:23:15 2021 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 chrI 10416569 1 N <DUP> 130.28 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=2;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69
--- a/test-data/result-6.vcf Sun Apr 18 17:08:22 2021 +0000 +++ b/test-data/result-6.vcf Sun May 09 17:09:33 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20200925 +##fileDate=20210508 ##reference=reference.fa ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> @@ -50,10 +50,10 @@ ##smoove_count_stats=celegans-2:2531,2421,134,276 ##source=LUMPY ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Fri Sep 25 09:37:11 2020 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:19:15 2021 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 -##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Fri Sep 25 09:37:11 2020 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:19:15 2021 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 chrI 10416569 1 N <DUP> 170.7 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69 1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
--- a/vcf2hrdetect.xml Sun Apr 18 17:08:22 2021 +0000 +++ b/vcf2hrdetect.xml Sun May 09 17:09:33 2021 +0000 @@ -1,5 +1,8 @@ -<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1"> +<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="2"> <description>to tabular hrdetect</description> + <requirements> + <requirement type="package" version="0.2.5">smoove</requirement> + </requirements> <macros> <import>macro_lumpy_smoove.xml</import> </macros> @@ -21,7 +24,7 @@ <tests> <test> <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" /> - <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" /> + <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" sort="true" ftype="tabular" /> </test> </tests> <help>