# HG changeset patch
# User iuc
# Date 1584802288 14400
# Node ID 9cb929f21cfaae14b890ad2a0b5c82b3559dd112
# Parent  fdba1586551d2d4a61647d0af505738a94b5d6a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"

diff -r fdba1586551d -r 9cb929f21cfa test-data/indel-call-out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/indel-call-out.vcf	Sat Mar 21 10:51:28 2020 -0400
@@ -0,0 +1,21 @@
+##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 
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##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