| Previous changeset 3:c27549b9aa1f (2020-05-29) Next changeset 5:426d707dfc47 (2020-10-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528" |
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modified:
lofreq_indelqual.xml macros.xml test-data/call-out1.vcf test-data/call-out2.vcf test-data/indel-call-out.vcf |
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| diff -r c27549b9aa1f -r 354b534eeab7 lofreq_indelqual.xml --- a/lofreq_indelqual.xml Fri May 29 15:25:46 2020 -0400 +++ b/lofreq_indelqual.xml Mon Jun 15 13:12:40 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="lofreq_indelqual" name="Insert indel qualities" version="@WRAPPER_VERSION@0"> +<tool id="lofreq_indelqual" name="Insert indel qualities" version="@TOOL_VERSION@+galaxy0"> <description>into a BAM file</description> <macros> <import>macros.xml</import> |
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| diff -r c27549b9aa1f -r 354b534eeab7 macros.xml --- a/macros.xml Fri May 29 15:25:46 2020 -0400 +++ b/macros.xml Mon Jun 15 13:12:40 2020 -0400 |
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| @@ -1,11 +1,11 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> - <token name="@TOOL_VERSION@">2.1.4</token> + <token name="@TOOL_VERSION@">2.1.5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement> <yield/> </requirements> + <version_command>lofreq version | grep version | cut -d ' ' -f 2</version_command> </xml> <xml name="citations"> <citations> |
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| diff -r c27549b9aa1f -r 354b534eeab7 test-data/call-out1.vcf --- a/test-data/call-out1.vcf Fri May 29 15:25:46 2020 -0400 +++ b/test-data/call-out1.vcf Mon Jun 15 13:12:40 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##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 +##fileDate=20200615 +##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpe0171355/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallell2yprl2k/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 c27549b9aa1f -r 354b534eeab7 test-data/call-out2.vcf --- a/test-data/call-out2.vcf Fri May 29 15:25:46 2020 -0400 +++ b/test-data/call-out2.vcf Mon Jun 15 13:12:40 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##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 +##fileDate=20200615 +##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallelg3dmyvln/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 c27549b9aa1f -r 354b534eeab7 test-data/indel-call-out.vcf --- a/test-data/indel-call-out.vcf Fri May 29 15:25:46 2020 -0400 +++ b/test-data/indel-call-out.vcf Mon Jun 15 13:12:40 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##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 +##fileDate=20200615 +##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/tmp265htsdc/job_working_directory/000/31/working/pp-tmp/lofreq2_call_parallel4gfado3q/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 . ;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 +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 |