# 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 @@
 <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>
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=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
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=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
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=<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
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