# HG changeset patch
# User iuc
# Date 1673430832 0
# Node ID 3e4f434a69c671b3ac58e7e6398862819bd71727
# Parent  e319b5b6587971694ad5f106a65ae8dd5cde5cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324

diff -r e319b5b65879 -r 3e4f434a69c6 ivar_consensus.xml
--- a/ivar_consensus.xml	Wed Jul 13 15:17:36 2022 +0000
+++ b/ivar_consensus.xml	Wed Jan 11 09:53:52 2023 +0000
@@ -1,10 +1,10 @@
-<tool id="ivar_consensus" name="ivar consensus" version="@VERSION@+galaxy0">
+<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Call consensus from aligned BAM file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         #import re
         #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
diff -r e319b5b65879 -r 3e4f434a69c6 macros.xml
--- a/macros.xml	Wed Jul 13 15:17:36 2022 +0000
+++ b/macros.xml	Wed Jan 11 09:53:52 2023 +0000
@@ -1,10 +1,14 @@
+<?xml version="1.0"?>
 <macros>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@TOOL_VERSION@">1.3.1</token>
+  <token name="@PROFILE@">21.01</token>
   <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="@VERSION@">ivar</requirement>
-      <yield />
-    </requirements>
+  <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">ivar</requirement>
+      <requirement type="package" version="3.10.8">python</requirement>
+      <requirement type="package" version="1.16">samtools</requirement>
+      <yield/>
+  </requirements>
   </xml>
   <xml name="version_command">
     <version_command>ivar version | grep version</version_command>
@@ -12,7 +16,7 @@
   <xml name="citations">
     <citations>
       <citation type="doi">10.1186/s13059-018-1618-7</citation>
-      <yield />
+      <yield/>
     </citations>
   </xml>
 </macros>
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52.consensus.fa.fai
--- a/test-data/zika/Z52.consensus.fa.fai	Wed Jul 13 15:17:36 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Consensus_Z52.consensus_threshold_0_quality_20	10139	48	10139	10140
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52.consensus.qual.txt
--- a/test-data/zika/Z52.consensus.qual.txt	Wed Jul 13 15:17:36 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
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diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_a.sorted.bam.bai
Binary file test-data/zika/Z52_a.sorted.bam.bai has changed
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_a.trimmed.sorted.bam.bai
Binary file test-data/zika/Z52_a.trimmed.sorted.bam.bai has changed
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_a.tsv
--- a/test-data/zika/Z52_a.tsv	Wed Jul 13 15:17:36 2022 +0000
+++ b/test-data/zika/Z52_a.tsv	Wed Jan 11 09:53:52 2023 +0000
@@ -9,7 +9,7 @@
 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	5680	C	T	27	10	44	8	3	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
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_a.vcf
--- a/test-data/zika/Z52_a.vcf	Wed Jul 13 15:17:36 2022 +0000
+++ b/test-data/zika/Z52_a.vcf	Wed Jan 11 09:53:52 2023 +0000
@@ -22,7 +22,7 @@
 PRV	3148	.	Y	T	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563
 PRV	3148	.	Y	C	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199
 PRV	3295	.	A	G	.	PASS	DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385
-PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=5;REF_QUAL=44;ALT_DP=8;ALT_RV=2;ALT_QUAL=46;AF=0.228571
+PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=10;REF_QUAL=44;ALT_DP=8;ALT_RV=3;ALT_QUAL=46;AF=0.228571
 PRV	5723	.	T	G	.	FAIL	DP=32;REF_DP=31;REF_RV=31;REF_QUAL=35;ALT_DP=1;ALT_RV=1;ALT_QUAL=21;AF=0.03125
 PRV	6201	.	A	G	.	FAIL	DP=12;REF_DP=10;REF_RV=0;REF_QUAL=35;ALT_DP=2;ALT_RV=0;ALT_QUAL=38;AF=0.166667
 PRV	6211	.	T	C	.	FAIL	DP=9;REF_DP=8;REF_RV=0;REF_QUAL=36;ALT_DP=1;ALT_RV=0;ALT_QUAL=35;AF=0.111111
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_a_annotated.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52_a_annotated.tsv	Wed Jan 11 09:53:52 2023 +0000
@@ -0,0 +1,17 @@
+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	cds-YP_002790881.1	AAA	K	TAA	*
+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	cds-YP_002790881.1	CTG	L	TTG	L
+PRV	1965	T	G	302	113	37	63	25	37	0.172603	365	4.41891e-21	TRUE	cds-YP_002790881.1	GTT	V	GGT	G
+PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE	cds-YP_002790881.1	AGA	R	GGA	G
+PRV	2781	T	G	354	70	37	48	8	36	0.117647	408	4.33605e-16	TRUE	cds-YP_002790881.1	GTG	V	GGG	G
+PRV	2922	C	T	264	0	36	11	0	36	0.04	275	0.000440953	TRUE	cds-YP_002790881.1	ACT	T	ATT	I
+PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	cds-YP_002790881.1	GAY	X	GAT	D
+PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE	cds-YP_002790881.1	GAY	X	GAC	D
+PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	cds-YP_002790881.1	GCA	A	GCG	A
+PRV	5680	C	T	27	10	44	8	3	46	0.228571	35	0.000596701	TRUE	cds-YP_002790881.1	TTC	F	TTT	F
+PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE	cds-YP_002790881.1	TGA	*	GGA	G
+PRV	6201	A	G	10	0	35	2	0	38	0.166667	12	0.26087	FALSE	cds-YP_002790881.1	GAA	E	GGA	G
+PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE	cds-YP_002790881.1	TGT	C	TGC	C
+PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	cds-YP_002790881.1	CAG	Q	TAG	*
+PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	cds-YP_002790881.1	CTT	L	TTT	F
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_a_pass.vcf
--- a/test-data/zika/Z52_a_pass.vcf	Wed Jul 13 15:17:36 2022 +0000
+++ b/test-data/zika/Z52_a_pass.vcf	Wed Jan 11 09:53:52 2023 +0000
@@ -19,6 +19,6 @@
 PRV	3148	.	Y	T	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563
 PRV	3148	.	Y	C	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199
 PRV	3295	.	A	G	.	PASS	DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385
-PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=5;REF_QUAL=44;ALT_DP=8;ALT_RV=2;ALT_QUAL=46;AF=0.228571
+PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=10;REF_QUAL=44;ALT_DP=8;ALT_RV=3;ALT_QUAL=46;AF=0.228571
 PRV	7916	.	C	T	.	PASS	DP=432;REF_DP=351;REF_RV=289;REF_QUAL=36;ALT_DP=81;ALT_RV=78;ALT_QUAL=37;AF=0.1875
 PRV	9713	.	C	T	.	PASS	DP=387;REF_DP=374;REF_RV=0;REF_QUAL=37;ALT_DP=13;ALT_RV=0;ALT_QUAL=35;AF=0.0335917
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_b.sorted.bam.bai
Binary file test-data/zika/Z52_b.sorted.bam.bai has changed
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/Z52_b.trimmed.sorted.bam.bai
Binary file test-data/zika/Z52_b.trimmed.sorted.bam.bai has changed
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/db/PRV.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/PRV.gff	Wed Jan 11 09:53:52 2023 +0000
@@ -0,0 +1,27 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ViralProj36615
+#!genome-build-accession NCBI_Assembly:GCF_000882815.3
+##sequence-region NC_012532.1 1 10794
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=64320
+NC_012532.1	RefSeq	region	1	10794	.	+	.	ID=NC_012532.1:1..10794;Dbxref=taxon:64320;country=Uganda;gbkey=Src;genome=genomic;mol_type=genomic RNA;nat-host=sentinel monkey;note=mosquito-borne flavivirus;strain=MR 766
+NC_012532.1	RefSeq	five_prime_UTR	1	106	.	+	.	ID=id-NC_012532.1:1..106;gbkey=5'UTR
+NC_012532.1	RefSeq	gene	107	10366	.	+	.	ID=gene-ZIKV_gp1;Dbxref=GeneID:7751225;Name=POLY;gbkey=Gene;gene=POLY;gene_biotype=protein_coding;locus_tag=ZIKV_gp1
+NC_012532.1	RefSeq	CDS	107	10366	.	+	0	ID=cds-YP_002790881.1;Parent=gene-ZIKV_gp1;Dbxref=Genbank:YP_002790881.1,GeneID:7751225;Name=YP_002790881.1;gbkey=CDS;gene=POLY;locus_tag=ZIKV_gp1;product=polyprotein;protein_id=YP_002790881.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	107	472	.	+	.	ID=id-YP_002790881.1:1..122;Parent=cds-YP_002790881.1;gbkey=Prot;product=anchored capsid protein ancC;protein_id=YP_009227206.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	107	418	.	+	.	ID=id-YP_002790881.1:1..104;Parent=cds-YP_002790881.1;gbkey=Prot;product=capsid protein C;protein_id=YP_009227196.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	473	976	.	+	.	ID=id-YP_002790881.1:123..290;Parent=cds-YP_002790881.1;gbkey=Prot;product=membrane glycoprotein precursor prM;protein_id=YP_009227197.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	473	751	.	+	.	ID=id-YP_002790881.1:123..215;Parent=cds-YP_002790881.1;gbkey=Prot;product=protein pr;protein_id=YP_009227207.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	752	976	.	+	.	ID=id-YP_002790881.1:216..290;Parent=cds-YP_002790881.1;gbkey=Prot;product=membrane glycoprotein M;protein_id=YP_009227208.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	977	2476	.	+	.	ID=id-YP_002790881.1:291..790;Parent=cds-YP_002790881.1;gbkey=Prot;product=envelope protein E;protein_id=YP_009227198.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	2477	3532	.	+	.	ID=id-YP_002790881.1:791..1142;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS1;protein_id=YP_009227199.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	3533	4210	.	+	.	ID=id-YP_002790881.1:1143..1368;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS2A;protein_id=YP_009227200.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	4211	4600	.	+	.	ID=id-YP_002790881.1:1369..1498;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS2B;protein_id=YP_009227201.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	4601	6451	.	+	.	ID=id-YP_002790881.1:1499..2115;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS3;protein_id=YP_009227202.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	6452	6832	.	+	.	ID=id-YP_002790881.1:2116..2242;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS4A;protein_id=YP_009227203.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	6833	6901	.	+	.	ID=id-YP_002790881.1:2243..2265;Parent=cds-YP_002790881.1;gbkey=Prot;product=protein 2K;protein_id=YP_009227209.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	6902	7654	.	+	.	ID=id-YP_002790881.1:2266..2516;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS4B;protein_id=YP_009227204.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	7655	10363	.	+	.	ID=id-YP_002790881.1:2517..3419;Parent=cds-YP_002790881.1;gbkey=Prot;product=RNA-dependent RNA polymerase NS5;protein_id=YP_009227205.1
+NC_012532.1	RefSeq	three_prime_UTR	10367	10794	.	+	.	ID=id-NC_012532.1:10367..10794;gbkey=3'UTR
+###
diff -r e319b5b65879 -r 3e4f434a69c6 test-data/zika/primer_mismatchers_indices.txt
--- a/test-data/zika/primer_mismatchers_indices.txt	Wed Jul 13 15:17:36 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-400_18_out_L**	400_23_out_R	400_32_out_L
\ No newline at end of file