# HG changeset patch # User iuc # Date 1633464375 0 # Node ID 17ad142b56e64d4de1dbed4dca1530f8f4544abf # Parent 07a6e49c7d74b97f2646974b1de94162b0e465b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4" diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_input.bam Binary file test-data/cv_input.bam has changed diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_output.gff --- /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 diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_output.txt --- /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 diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_output.vcf --- /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= +##FILTER= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#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 diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_qualityhist_output.tabular --- /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 diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_scorehist_output.tabular --- /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 diff -r 07a6e49c7d74 -r 17ad142b56e6 test-data/cv_zygosityhist_output.tabular --- /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