| Previous changeset 2:cdaab621d454 (2020-03-21) Next changeset 4:af7e416d8176 (2020-06-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a" |
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modified:
macros.xml test-data/alnqual-out1.bam test-data/alnqual-out2.bam test-data/alnqual-out3.bam test-data/alnqual-out4.bam test-data/alnqual-out5.bam test-data/call-out1.vcf test-data/call-out2.vcf test-data/indel-call-out.vcf test-data/indelqual-out1.bam test-data/indelqual-out2.bam test-data/indelqual-out3.bam |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 macros.xml --- a/macros.xml Sat Mar 21 10:50:52 2020 -0400 +++ b/macros.xml Fri May 29 15:24:28 2020 -0400 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> - <token name="@TOOL_VERSION@">2.1.3.1</token> + <token name="@TOOL_VERSION@">2.1.4</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement> |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/alnqual-out1.bam |
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| Binary file test-data/alnqual-out1.bam has changed |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/alnqual-out2.bam |
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| Binary file test-data/alnqual-out2.bam has changed |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/alnqual-out3.bam |
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| Binary file test-data/alnqual-out3.bam has changed |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/alnqual-out4.bam |
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| Binary file test-data/alnqual-out4.bam has changed |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/alnqual-out5.bam |
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| Binary file test-data/alnqual-out5.bam has changed |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/call-out1.vcf --- a/test-data/call-out1.vcf Sat Mar 21 10:50:52 2020 -0400 +++ b/test-data/call-out1.vcf Fri May 29 15:24:28 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##fileDate=20191125 -##source=lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallel3mrmthi_/0.vcf.gz alignments.bam +##fileDate=20200529 +##source=lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelqgn6kxdr/0.vcf.gz reads.bam ##reference=reference.fa ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/call-out2.vcf --- a/test-data/call-out2.vcf Sat Mar 21 10:50:52 2020 -0400 +++ b/test-data/call-out2.vcf Fri May 29 15:24:28 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##fileDate=20191204 -##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpjsbggC/job_working_directory/000/8/working/pp-tmp/lofreq2_call_parallelj9yxuugx/0.vcf.gz reads.bam +##fileDate=20200529 +##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelkzkzyltj/0.vcf.gz reads.bam ##reference=reference.fa ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/indel-call-out.vcf --- a/test-data/indel-call-out.vcf Sat Mar 21 10:50:52 2020 -0400 +++ b/test-data/indel-call-out.vcf Fri May 29 15:24:28 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##fileDate=20200320 -##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmppZpVLj/job_working_directory/000/9/working/pp-tmp/lofreq2_call_parallele60ipsuv/0.vcf.gz reads.bam +##fileDate=20200529 +##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelafbznae0/0.vcf.gz reads.bam ##reference=reference.fa ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> @@ -10,12 +10,12 @@ ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> #CHROM POS ID REF ALT QUAL FILTER INFO -pBR322 725 . G GN 0 . DP=46;AF=0.021739;SB=0;DP4=22,23,0,1;INDEL;HRUN=1 -pBR322 746 . A AN 0 . DP=225;AF=0.004444;SB=3;DP4=116,108,0,1;INDEL;HRUN=1 -pBR322 747 . T TN 0 . DP=230;AF=0.004348;SB=3;DP4=118,111,0,1;INDEL;HRUN=1 -pBR322 751 . G GN 0 . DP=255;AF=0.003922;SB=3;DP4=128,126,0,1;INDEL;HRUN=1 -pBR322 807 . T TN 0 . DP=606;AF=0.001650;SB=0;DP4=300,305,0,1;INDEL;HRUN=3 -pBR322 943 . C CCG 0 . DP=1465;AF=0.000683;SB=0;DP4=709,755,0,1;INDEL;HRUN=1 -pBR322 1152 . C CN 0 . DP=1754;AF=0.000570;SB=0;DP4=926,830,1,0;INDEL;HRUN=2 -pBR322 1271 . A AN 0 . DP=1743;AF=0.000574;SB=0;DP4=890,855,1,0;INDEL;HRUN=2 -pBR322 1376 . A ANN 0 . DP=1691;AF=0.000591;SB=3;DP4=849,843,0,1;INDEL;HRUN=1 +pBR322 725 . G GN 0 . ;HRUN=1 +pBR322 746 . A AN 0 . ;HRUN=1 +pBR322 747 . T TN 0 . ;HRUN=1 +pBR322 751 . G GN 0 . ;HRUN=1 +pBR322 807 . T TN 0 . ;HRUN=3 +pBR322 943 . C CCG 0 . ;HRUN=1 +pBR322 1152 . C CN 0 . ;HRUN=2 +pBR322 1271 . A AN 0 . ;HRUN=2 +pBR322 1376 . A ANN 0 . ;HRUN=1 |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/indelqual-out1.bam |
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| Binary file test-data/indelqual-out1.bam has changed |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/indelqual-out2.bam |
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| diff -r cdaab621d454 -r dbd9f2db9ed8 test-data/indelqual-out3.bam |
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| Binary file test-data/indelqual-out3.bam has changed |