# HG changeset patch
# User iuc
# Date 1586017511 14400
# Node ID a38934e303b9e8a1b2c727c027788b85a3231a58
# Parent  f362150bef4190e9ca3f75a032082ba106c540a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27fa363aa1289366fd0e888709d022357533e4de"

diff -r f362150bef41 -r a38934e303b9 macros.xml
--- a/macros.xml	Mon Mar 30 06:37:01 2020 -0400
+++ b/macros.xml	Sat Apr 04 12:25:11 2020 -0400
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.0.1</token>
+  <token name="@VERSION@">1.2</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@VERSION@">ivar</requirement>
diff -r f362150bef41 -r a38934e303b9 test-data/zika/Z52.tsv
--- a/test-data/zika/Z52.tsv	Mon Mar 30 06:37:01 2020 -0400
+++ b/test-data/zika/Z52.tsv	Sat Apr 04 12:25:11 2020 -0400
@@ -1,11 +1,11 @@
-REGION	POS	REF	ALT	REF_DP_Z52_a.tsv	REF_RV_Z52_a.tsv	REF_QUAL_Z52_a.tsv	ALT_DP_Z52_a.tsv	ALT_RV_Z52_a.tsv	ALT_QUAL_Z52_a.tsv	ALT_FREQ_Z52_a.tsv	TOTAL_DP_Z52_a.tsv	PVAL_Z52_a.tsv	PASS_Z52_a.tsv	REF_DP_Z52_b.tsv	REF_RV_Z52_b.tsv	REF_QUAL_Z52_b.tsv	ALT_DP_Z52_b.tsv	ALT_RV_Z52_b.tsv	ALT_QUAL_Z52_b.tsv	ALT_FREQ_Z52_b.tsv	TOTAL_DP_Z52_b.tsv	PVAL_Z52_b.tsv	PASS_Z52_b.tsv	
-PRV	1682	C	T	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE	1505	1475	37	50	50	37	0.0321543	1555	1.59703e-14	TRUE	
-PRV	1965	T	G	302	113	37	41	3	35	0.119534	343	2.81419e-14	TRUE	469	28	36	71	1	36	0.131481	540	1.31011e-23	TRUE	
-PRV	2781	T	G	353	70	37	48	8	36	0.117936	407	4.05758e-16	TRUE	404	75	37	35	7	36	0.0788288	444	1.12705e-11	TRUE	
-PRV	2922	C	T	263	0	36	11	0	36	0.040146	274	0.000431954	TRUE	277	0	36	19	0	34	0.0641892	296	1.46245e-06	TRUE	
-PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE	0	0	0	679	99	37	0.258765	2624	0	TRUE	
-PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	0	0	0	1943	271	36	0.740473	2624	0	TRUE	
-PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	1806	1806	36	69	69	34	0.0368	1875	2.28815e-20	TRUE	
-PRV	5680	C	T	27	5	44	8	2	45	0.228571	35	0.000596701	TRUE	38	5	50	7	1	49	0.155556	45	0.00133612	TRUE	
-PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	286	227	36	45	38	37	0.135952	331	4.31473e-15	TRUE	
-PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	475	0	37	27	0	36	0.0537849	502	4.66646e-09	TRUE	
+REGION	POS	REF	ALT	GFF_FEATURE	REF_CODON	REF_AA	ALT_CODON	ALT_AA	REF_DP_./var_0.tsv	REF_RV_./var_0.tsv	REF_QUAL_./var_0.tsv	ALT_DP_./var_0.tsv	ALT_RV_./var_0.tsv	ALT_QUAL_./var_0.tsv	ALT_FREQ_./var_0.tsv	TOTAL_DP_./var_0.tsv	PVAL_./var_0.tsv	PASS_./var_0.tsv	REF_DP_./var_1.tsv	REF_RV_./var_1.tsv	REF_QUAL_./var_1.tsv	ALT_DP_./var_1.tsv	ALT_RV_./var_1.tsv	ALT_QUAL_./var_1.tsv	ALT_FREQ_./var_1.tsv	TOTAL_DP_./var_1.tsv	PVAL_./var_1.tsv	PASS_./var_1.tsv	
+PRV	1682	C	T	1505	1475	37	50	50	37	0.0321543	1555	1.59703e-14	TRUE	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE
+PRV	1965	T	G	469	28	36	71	1	36	0.131481	540	1.31011e-23	TRUE	302	113	37	41	3	35	0.119534	343	2.81419e-14	TRUE
+PRV	2781	T	G	404	75	37	35	7	36	0.0788288	444	1.12705e-11	TRUE	353	70	37	48	8	36	0.117936	407	4.05758e-16	TRUE
+PRV	2922	C	T	277	0	36	19	0	34	0.0641892	296	1.46245e-06	TRUE	263	0	36	11	0	36	0.040146	274	0.000431954	TRUE
+PRV	3148	Y	C	0	0	0	679	99	37	0.258765	2624	0	TRUE	0	0	0	381	75	36	0.223199	1707	0	TRUE
+PRV	3148	Y	T	0	0	0	1943	271	36	0.740473	2624	0	TRUE	0	0	0	1324	264	36	0.77563	1707	0	TRUE
+PRV	3295	A	G	1806	1806	36	69	69	34	0.0368	1875	2.28815e-20	TRUE	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE
+PRV	5680	C	T	38	5	50	7	1	49	0.155556	45	0.00133612	TRUE	27	5	44	8	2	45	0.228571	35	0.000596701	TRUE
+PRV	7916	C	T	286	227	36	45	38	37	0.135952	331	4.31473e-15	TRUE	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE
+PRV	9713	C	T	475	0	37	27	0	36	0.0537849	502	4.66646e-09	TRUE	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE
diff -r f362150bef41 -r a38934e303b9 test-data/zika/Z52_a.tsv
--- a/test-data/zika/Z52_a.tsv	Mon Mar 30 06:37:01 2020 -0400
+++ b/test-data/zika/Z52_a.tsv	Sat Apr 04 12:25:11 2020 -0400
@@ -1,17 +1,17 @@
-REGION	POS	REF	ALT	REF_DP	REF_RV	REF_QUAL	ALT_DP	ALT_RV	ALT_QUAL	ALT_FREQ	TOTAL_DP	PVAL	PASS
-PRV	350	A	T	101	101	36	5	5	35	0.0471698	106	0.0304989	FALSE
-PRV	722	C	+A	280	234	36	9	0	20	0.0319149	282	0.0349042	FALSE
-PRV	1682	C	T	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE
-PRV	1965	T	G	302	113	37	41	3	35	0.119534	343	2.81419e-14	TRUE
-PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE
-PRV	2781	T	G	353	70	37	48	8	36	0.117936	407	4.05758e-16	TRUE
-PRV	2922	C	T	263	0	36	11	0	36	0.040146	274	0.000431954	TRUE
-PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE
-PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE
-PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE
-PRV	5680	C	T	27	5	44	8	2	45	0.228571	35	0.000596701	TRUE
-PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE
-PRV	6201	A	G	10	0	35	2	0	25	0.166667	12	0.26087	FALSE
-PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE
-PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE
-PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE
+REGION	POS	REF	ALT	REF_DP	REF_RV	REF_QUAL	ALT_DP	ALT_RV	ALT_QUAL	ALT_FREQ	TOTAL_DP	PVAL	PASS	GFF_FEATURE	REF_CODON	REF_AA	ALT_CODON	ALT_AA
+PRV	350	A	T	101	101	36	5	5	35	0.0471698	106	0.0304989	FALSE	NA	NA	NA	NA	NA
+PRV	722	C	+A	280	234	36	9	0	20	0.0319149	282	0.0349042	FALSE	NA	NA	NA	NA	NA
+PRV	1682	C	T	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE	NA	NA	NA	NA	NA
+PRV	1965	T	G	302	113	37	63	25	37	0.172603	365	4.41891e-21	TRUE	NA	NA	NA	NA	NA
+PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE	NA	NA	NA	NA	NA
+PRV	2781	T	G	354	70	37	48	8	36	0.117647	408	4.33605e-16	TRUE	NA	NA	NA	NA	NA
+PRV	2922	C	T	264	0	36	11	0	36	0.04	275	0.000440953	TRUE	NA	NA	NA	NA	NA
+PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	NA	NA	NA	NA	NA
+PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE	NA	NA	NA	NA	NA
+PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	NA	NA	NA	NA	NA
+PRV	5680	C	T	27	5	44	8	2	46	0.228571	35	0.000596701	TRUE	NA	NA	NA	NA	NA
+PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE	NA	NA	NA	NA	NA
+PRV	6201	A	G	10	0	35	2	0	38	0.166667	12	0.26087	FALSE	NA	NA	NA	NA	NA
+PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE	NA	NA	NA	NA	NA
+PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	NA	NA	NA	NA	NA
+PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	NA	NA	NA	NA	NA
diff -r f362150bef41 -r a38934e303b9 test-data/zika/primer_mismatchers_indices.txt
--- a/test-data/zika/primer_mismatchers_indices.txt	Mon Mar 30 06:37:01 2020 -0400
+++ b/test-data/zika/primer_mismatchers_indices.txt	Sat Apr 04 12:25:11 2020 -0400
@@ -1,1 +1,1 @@
-400_18_out_L**	400_18_out_R**	400_23_out_R	400_23_out_L	400_32_out_L	400_32_out_R
\ No newline at end of file
+400_18_out_L**	400_23_out_R	400_32_out_L
\ No newline at end of file