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changeset 119:2fff478aca4b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d4f36c410e14bec8bf5a42ea4ff20e2ae4db5897
author bgruening
date Sat, 21 Sep 2024 06:13:01 +0000
parents 794aecef8327
children af482048ca1a
files __pycache__/jbrowse2.cpython-312.pyc foo foo.tbi test-data/vcf/merlin.vcf.2 test-data/vcf/merlinold.vcf
diffstat 5 files changed, 0 insertions(+), 46 deletions(-) [+]
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Binary file __pycache__/jbrowse2.cpython-312.pyc has changed
Binary file foo has changed
Binary file foo.tbi has changed
--- a/test-data/vcf/merlin.vcf.2	Sat Sep 21 04:01:38 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##fileDate=20090805
-##source=myImputationProgramV3.1
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
-##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
-##FILTER=<ID=q10,Description="Quality below 10">
-##FILTER=<ID=s50,Description="Less than 50% of samples have data">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-Merlin	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
-Merlin	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
-Merlin	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
-Merlin	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
-Merlin	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
--- a/test-data/vcf/merlinold.vcf	Sat Sep 21 04:01:38 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##fileDate=20090805
-##source=myImputationProgramV3.1
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number	of	Samples	With	Data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total	Depth">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele	Frequency">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral	Allele">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP	membership,	build	129">
-##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2	membership">
-##FILTER=<ID=q10,Description="Quality	below	10">
-##FILTER=<ID=s50,Description="Less	than	50%	of	samples	have	data">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype	Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read	Depth">
-##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype	Quality">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-Merlin	61	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
-Merlin	122	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
-Merlin	488	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
-Merlin	549	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
-Merlin	1098	microsat1		G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3