changeset 1:17ad142b56e6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
author iuc
date Tue, 05 Oct 2021 20:06:15 +0000
parents 07a6e49c7d74
children e0ca2ec4f5d9
files test-data/cv_input.bam test-data/cv_output.gff test-data/cv_output.txt test-data/cv_output.vcf test-data/cv_qualityhist_output.tabular test-data/cv_scorehist_output.tabular test-data/cv_zygosityhist_output.tabular
diffstat 7 files changed, 184 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file test-data/cv_input.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.gff	Tue Oct 05 20:06:15 2021 +0000
@@ -0,0 +1,18 @@
+##gff-version
+#BBMapVersion
+#ploidy	2
+#rarity	1.00000
+#minAlleleFraction	0.1000
+#reads	2207
+#pairedReads	0
+#properlyPairedReads	0
+#readLengthAvg
+#properPairRate	0.0000
+#totalQualityAvg
+#mapqAvg
+#reference
+#seqid	source	type	start	end	score	strand	phase	attributes
+NC_002945.4	.	sequence_variant_obs	976327	976327
+NC_002945.4	.	sequence_variant_obs	1501932	1501932
+NC_002945.4	.	sequence_variant_obs	3380579	3380579
+NC_002945.4	.	sequence_variant_obs	3646293	3646293
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.txt	Tue Oct 05 20:06:15 2021 +0000
@@ -0,0 +1,18 @@
+#fileformat
+#BBMapVersion
+#ploidy	2
+#rarity	1.00000
+#minAlleleFraction	0.1000
+#reads	2207
+#pairedReads	0
+#properlyPairedReads	0
+#readLengthAvg
+#properPairRate
+#totalQualityAvg
+#mapqAvg
+#reference
+#scaf	start	stop	type	call	r1p	r1m	r2p	r2m	paired	lengthSum	mapq	mapqMax	baseq	baseqMax	edist	edistMax	id	idMax	cov	minusCov	nearbyVarCount	flagged	contigEndDist	phredScore	readCount	alleleFraction	revisedAF	strandRatio	baseqAvg	mapqAvg	edistAvg	identityAvg	edistScore	identityScore	qualityScore	pairedScore	biasScore	coverageScore	homopolymerScore	score
+0	976326	976327	SUB	T
+0	1501931	1501932	SUB	C
+0	3380578	3380579	SUB	G
+0	3646292	3646293	SUB	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.vcf	Tue Oct 05 20:06:15 2021 +0000
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.2
+##BBMapVersion=
+##ploidy=2
+##rarity=1.00000
+##minallelefraction=0.10000
+##reads=2207
+##pairedReads=0
+##properlyPairedReads=0
+##readLengthAvg=
+##properPairRate=0.00000
+##totalQualityAvg=
+##mapqAvg=43.348
+##reference=
+##contig=<ID=NC_002945.4,length=7000>
+##FILTER=<ID=FAIL,Description="Fail">
+##FILTER=<ID=PASS,Description="Pass">
+##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number">
+##INFO=<ID=STA,Number=1,Type=Integer,Description="Start">
+##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop">
+##INFO=<ID=TYP,Number=1,Type=String,Description="Type">
+##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count">
+##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count">
+##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count">
+##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count">
+##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage">
+##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
+##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
+##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum">
+##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum">
+##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max">
+##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum">
+##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max">
+##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum">
+##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max">
+##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum">
+##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max">
+##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
+##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
+##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance">
+##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
+##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
+##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
+##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
+##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
+##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	
+NC_002945.4	976327	.	N	T	22.21	PASS	SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
+NC_002945.4	1501932	.	N	C	27.20	PASS	SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
+NC_002945.4	3380579	.	N	G	27.85	PASS	SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
+NC_002945.4	3646293	.	N	A	23.34	PASS	SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_qualityhist_output.tabular	Tue Oct 05 20:06:15 2021 +0000
@@ -0,0 +1,46 @@
+#BaseQualityHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality	AvgCount	MaxCount
+0	0	0
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	0	0
+7	0	0
+8	0	0
+9	0	0
+10	0	0
+11	0	0
+12	0	0
+13	0	0
+14	0	0
+15	0	0
+16	0	0
+17	0	0
+18	0	0
+19	0	0
+20	0	0
+21	0	0
+22	0	0
+23	0	0
+24	1	1
+25	0	0
+26	0	0
+27	0	0
+28	0	0
+29	0	0
+30	0	0
+31	0	0
+32	1	0
+33	0	0
+34	0	0
+35	0	0
+36	0	0
+37	1	0
+38	1	2
+39	0	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_scorehist_output.tabular	Tue Oct 05 20:06:15 2021 +0000
@@ -0,0 +1,34 @@
+#ScoreHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality	Count
+0	0
+1	0
+2	0
+3	0
+4	0
+5	0
+6	0
+7	0
+8	0
+9	0
+10	0
+11	0
+12	0
+13	0
+14	0
+15	0
+16	0
+17	0
+18	0
+19	0
+20	0
+21	0
+22	1
+23	1
+24	0
+25	0
+26	0
+27	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_zygosityhist_output.tabular	Tue Oct 05 20:06:15 2021 +0000
@@ -0,0 +1,8 @@
+#ZygoHist
+#Vars
+#Mean
+#HomozygousFraction
+#Zygosity	Count
+0	0
+1	0
+2	4