Mercurial > repos > artbio > lumpy_smoove

changeset 9:7dcf61950215 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 5f62b58c65917afbb018296568c81ad132106012
author artbio
date Wed, 05 Apr 2023 15:56:13 +0000
parents b4dec06d8fc6
children 8711df965d4b
files lumpy_smoove.xml test-data/result-1.vcf test-data/result-2.vcf test-data/result-3.vcf test-data/result-6.vcf vcf2hrdetect.py vcf2hrdetect.xml
diffstat 7 files changed, 34 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- a/lumpy_smoove.xml	Sun May 09 17:09:33 2021 +0000
+++ b/lumpy_smoove.xml	Wed Apr 05 15:56:13 2023 +0000
@@ -1,10 +1,11 @@
-<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy8">
+<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.8+galaxy0">
     <description>find structural variants using the smoove workflow</description>
     <macros>
         <import>macro_lumpy_smoove.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.2.5">smoove</requirement>
+        <requirement type="package" version="0.7.1">svtyper</requirement>
+        <requirement type="package" version="0.2.8">smoove</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
--- a/test-data/result-1.vcf	Sun May 09 17:09:33 2021 +0000
+++ b/test-data/result-1.vcf	Wed Apr 05 15:56:13 2023 +0000
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20210508
+##fileDate=20230405
 ##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">
@@ -45,15 +45,15 @@
 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
 ##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_version=0.2.8
 ##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=Sat May  8 19:20:12 2021
+##bcftools_annotateVersion=1.16+htslib-1.17
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr  5 16:07:34 2023
 ##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=Sat May  8 19:20:12 2021
+##bcftools_viewVersion=1.16+htslib-1.17
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr  5 16:07:34 2023
 #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 May 09 17:09:33 2021 +0000
+++ b/test-data/result-2.vcf	Wed Apr 05 15:56:13 2023 +0000
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20210508
+##fileDate=20230405
 ##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">
@@ -45,15 +45,15 @@
 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
 ##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_version=0.2.8
 ##smoove_count_stats=celegans-1:2869,2691,202,330
+##smoove_count_stats=celegans-2:2531,2421,156,296
 ##source=LUMPY
-##bcftools_annotateVersion=1.10.2+htslib-1.10.2
-##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May  8 19:20:59 2021
+##bcftools_annotateVersion=1.16+htslib-1.17
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr  5 13:40:08 2023
 ##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=Sat May  8 19:20:59 2021
+##bcftools_viewVersion=1.16+htslib-1.17
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr  5 13:40:08 2023
 #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 May 09 17:09:33 2021 +0000
+++ b/test-data/result-3.vcf	Wed Apr 05 15:56:13 2023 +0000
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20210508
+##fileDate=20230405
 ##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">
@@ -45,15 +45,15 @@
 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
 ##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_version=0.2.8
 ##smoove_count_stats=celegans-1:2869,2691,202,330
+##smoove_count_stats=celegans-2:2531,2421,156,296
 ##source=LUMPY
-##bcftools_annotateVersion=1.10.2+htslib-1.10.2
-##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May  8 19:21:48 2021
+##bcftools_annotateVersion=1.16+htslib-1.17
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr  5 13:41:07 2023
 ##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=Sat May  8 19:21:48 2021
+##bcftools_viewVersion=1.16+htslib-1.17
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr  5 13:41:07 2023
 #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-6.vcf	Sun May 09 17:09:33 2021 +0000
+++ b/test-data/result-6.vcf	Wed Apr 05 15:56:13 2023 +0000
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20210508
+##fileDate=20230405
 ##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">
@@ -45,15 +45,15 @@
 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
 ##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_version=0.2.8
 ##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=Sat May  8 19:19:15 2021
+##bcftools_annotateVersion=1.16+htslib-1.17
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr  5 16:06:25 2023
 ##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=Sat May  8 19:19:15 2021
+##bcftools_viewVersion=1.16+htslib-1.17
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr  5 16:06:25 2023
 #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.py	Sun May 09 17:09:33 2021 +0000
+++ b/vcf2hrdetect.py	Wed Apr 05 15:56:13 2023 +0000
@@ -26,7 +26,7 @@
                               chrom, coordbreak, "TRA"]
 for id in list(vcfdict):
     if "_" in id:
-        del(vcfdict[id])
+        del vcfdict[id]
 for id in vcfdict.keys():  # only sv that are not of type TRA or INV
     chr1 = vcfdict[id][0]
     chr2 = vcfdict[id][0]
--- a/vcf2hrdetect.xml	Sun May 09 17:09:33 2021 +0000
+++ b/vcf2hrdetect.xml	Wed Apr 05 15:56:13 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="2">
+<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="3">
     <description>to tabular hrdetect</description>
     <requirements>
-        <requirement type="package" version="0.2.5">smoove</requirement>
+        <requirement type="package" version="0.2.8">smoove</requirement>
     </requirements>
     <macros>
         <import>macro_lumpy_smoove.xml</import>