# HG changeset patch # User iuc # Date 1590780346 14400 # Node ID c27549b9aa1f319620f1e1b087e4c1dc1b8fc38f # Parent f4473557ffc7037c1645022726ae9bf20b8066db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a" diff -r f4473557ffc7 -r c27549b9aa1f macros.xml --- a/macros.xml Sat Mar 21 10:51:47 2020 -0400 +++ b/macros.xml Fri May 29 15:25:46 2020 -0400 @@ -1,6 +1,6 @@ @TOOL_VERSION@+galaxy - 2.1.3.1 + 2.1.4 lofreq diff -r f4473557ffc7 -r c27549b9aa1f test-data/alnqual-out1.bam Binary file test-data/alnqual-out1.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/alnqual-out2.bam Binary file test-data/alnqual-out2.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/alnqual-out3.bam Binary file test-data/alnqual-out3.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/alnqual-out4.bam Binary file test-data/alnqual-out4.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/alnqual-out5.bam Binary file test-data/alnqual-out5.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/call-out1.vcf --- a/test-data/call-out1.vcf Sat Mar 21 10:51:47 2020 -0400 +++ b/test-data/call-out1.vcf Fri May 29 15:25:46 2020 -0400 @@ -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= ##INFO= diff -r f4473557ffc7 -r c27549b9aa1f test-data/call-out2.vcf --- a/test-data/call-out2.vcf Sat Mar 21 10:51:47 2020 -0400 +++ b/test-data/call-out2.vcf Fri May 29 15:25:46 2020 -0400 @@ -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= ##INFO= diff -r f4473557ffc7 -r c27549b9aa1f test-data/indel-call-out.vcf --- a/test-data/indel-call-out.vcf Sat Mar 21 10:51:47 2020 -0400 +++ b/test-data/indel-call-out.vcf Fri May 29 15:25:46 2020 -0400 @@ -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= ##INFO= @@ -10,12 +10,12 @@ ##INFO= ##INFO= #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 diff -r f4473557ffc7 -r c27549b9aa1f test-data/indelqual-out1.bam Binary file test-data/indelqual-out1.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/indelqual-out2.bam Binary file test-data/indelqual-out2.bam has changed diff -r f4473557ffc7 -r c27549b9aa1f test-data/indelqual-out3.bam Binary file test-data/indelqual-out3.bam has changed