# HG changeset patch
# User iuc
# Date 1724753651 0
# Node ID 770bceda77854c26cd883a53a77457d02dbe3c25
# Parent 1baa4ad1ac2f9f95c3bf83fae5409a78505149ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
diff -r 1baa4ad1ac2f -r 770bceda7785 bbnorm.xml
--- a/bbnorm.xml Sat May 18 19:13:59 2024 +0000
+++ b/bbnorm.xml Tue Aug 27 10:14:11 2024 +0000
@@ -145,22 +145,22 @@
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diff -r 1baa4ad1ac2f -r 770bceda7785 macros.xml
--- a/macros.xml Sat May 18 19:13:59 2024 +0000
+++ b/macros.xml Tue Aug 27 10:14:11 2024 +0000
@@ -1,15 +1,19 @@
- 39.06
- 2
+ 39.08
+ 0
22.01
- topic_0622
- topic_0091
+ topic_0622
+
+ topic_0091
+
- operation_0496
- operation_0491
+ operation_0496
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+ operation_0491
+
@@ -20,7 +24,8 @@
bbmap
- samtools
+ samtools
+
@@ -62,7 +67,7 @@
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@@ -87,18 +92,18 @@
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diff -r 1baa4ad1ac2f -r 770bceda7785 test-data/cv_output.gff
--- a/test-data/cv_output.gff Sat May 18 19:13:59 2024 +0000
+++ b/test-data/cv_output.gff Tue Aug 27 10:14:11 2024 +0000
@@ -1,18 +1,18 @@
-##gff-version
-#BBMapVersion
+##gff-version 3
+#BBMapVersion 39.08
#ploidy 2
#rarity 1.00000
#minAlleleFraction 0.1000
#reads 2207
#pairedReads 0
#properlyPairedReads 0
-#readLengthAvg
+#readLengthAvg 145.46
#properPairRate 0.0000
-#totalQualityAvg
-#mapqAvg
-#reference
+#totalQualityAvg 36.5800
+#mapqAvg 43.35
+#reference /home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
#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
+NC_002945.4 . sequence_variant_obs 976327 976327 0.87 + . ID=SUB T
+NC_002945.4 . sequence_variant_obs 1501932 1501932 0.92 + . ID=SUB C
+NC_002945.4 . sequence_variant_obs 3380579 3380579 0.92 + . ID=SUB G
+NC_002945.4 . sequence_variant_obs 3646293 3646293 0.89 + . ID=SUB A
diff -r 1baa4ad1ac2f -r 770bceda7785 test-data/cv_output.txt
--- a/test-data/cv_output.txt Sat May 18 19:13:59 2024 +0000
+++ b/test-data/cv_output.txt Tue Aug 27 10:14:11 2024 +0000
@@ -1,18 +1,18 @@
-#fileformat
-#BBMapVersion
+#fileformat Var_1.3
+#BBMapVersion 39.08
#ploidy 2
#rarity 1.00000
#minAlleleFraction 0.1000
#reads 2207
#pairedReads 0
#properlyPairedReads 0
-#readLengthAvg
-#properPairRate
-#totalQualityAvg
-#mapqAvg
-#reference
+#readLengthAvg 145.46
+#properPairRate 0.0000
+#totalQualityAvg 36.5800
+#mapqAvg 43.35
+#reference /home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
#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
+0 976326 976327 SUB T 2 0 0 0 0 292 77 40 48 24 111 65 1930 972 0 -1 0 0 0 22.21 2 1 1 0.5000 24 38.50 55.50 965 0.9972 0.9932 0.7489 0.9800 0.9737 0.7143 1 0.8725
+0 1501931 1501932 SUB C 0 2 0 0 0 292 88 44 64 39 74 38 1986 993 0 -1 0 0 0 27.20 2 1 1 0.5000 32 44 37 993 0.9851 0.9994 0.9831 0.9800 0.9737 0.7143 1 0.9202
+0 3380578 3380579 SUB G 0 2 0 0 0 289 87 44 75 38 105 63 1986 993 0 -1 0 0 0 27.85 2 1 1 0.5000 37.50 43.50 52.50 993 0.9968 0.9994 0.9972 0.9800 0.9737 0.7143 1 0.9250
+0 3646292 3646293 SUB A 1 1 0 0 0 291 86 44 76 38 44 31 1986 993 0 -1 0 0 0 23.34 2 1 1 1 38 43 22 993 0.7996 0.9994 0.9975 0.9800 0.9747 0.7143 1 0.8853
diff -r 1baa4ad1ac2f -r 770bceda7785 test-data/cv_output.vcf
--- a/test-data/cv_output.vcf Sat May 18 19:13:59 2024 +0000
+++ b/test-data/cv_output.vcf Tue Aug 27 10:14:11 2024 +0000
@@ -1,16 +1,16 @@
##fileformat=VCFv4.2
-##BBMapVersion=
+##BBMapVersion=39.08
##ploidy=2
##rarity=1.00000
##minallelefraction=0.10000
##reads=2207
##pairedReads=0
##properlyPairedReads=0
-##readLengthAvg=
+##readLengthAvg=145.462
##properPairRate=0.00000
-##totalQualityAvg=
+##totalQualityAvg=36.580
##mapqAvg=43.348
-##reference=
+##reference=/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
##contig=
##FILTER=
##FILTER=
@@ -53,8 +53,8 @@
##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
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT dataset_4f1db038-76fe-46bc-a222-dfc4894a8ff2.dat
+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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:22.21: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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:27.20: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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:27.85: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;RAF=1;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 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:1:23.34:PASS
diff -r 1baa4ad1ac2f -r 770bceda7785 test-data/cv_qualityhist_output.tabular
--- a/test-data/cv_qualityhist_output.tabular Sat May 18 19:13:59 2024 +0000
+++ b/test-data/cv_qualityhist_output.tabular Tue Aug 27 10:14:11 2024 +0000
@@ -1,8 +1,8 @@
#BaseQualityHist
-#Vars
-#Mean
-#Median
-#Mode
+#Vars 4
+#Mean 32.75
+#Median 32
+#Mode 32
#Quality AvgCount MaxCount
0 0 0
1 0 0
diff -r 1baa4ad1ac2f -r 770bceda7785 test-data/cv_scorehist_output.tabular
--- a/test-data/cv_scorehist_output.tabular Sat May 18 19:13:59 2024 +0000
+++ b/test-data/cv_scorehist_output.tabular Tue Aug 27 10:14:11 2024 +0000
@@ -1,8 +1,8 @@
#ScoreHist
-#Vars
-#Mean
-#Median
-#Mode
+#Vars 4
+#Mean 24.75
+#Median 23
+#Mode 27
#Quality Count
0 0
1 0
diff -r 1baa4ad1ac2f -r 770bceda7785 test-data/cv_zygosityhist_output.tabular
--- a/test-data/cv_zygosityhist_output.tabular Sat May 18 19:13:59 2024 +0000
+++ b/test-data/cv_zygosityhist_output.tabular Tue Aug 27 10:14:11 2024 +0000
@@ -1,7 +1,7 @@
#ZygoHist
-#Vars
-#Mean
-#HomozygousFraction
+#Vars 4
+#Mean 2.000
+#HomozygousFraction 1.000
#Zygosity Count
0 0
1 0