Repository 'ivar_filtervariants'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants

Changeset 11:72ddd32392cd (2023-01-11)
Previous changeset 10:0135f1d487a0 (2022-07-13) Next changeset 12:8f8df367470d (2023-02-13)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
modified:
ivar_filtervariants.xml
macros.xml
test-data/zika/Z52_a.tsv
test-data/zika/Z52_a.vcf
test-data/zika/Z52_a_pass.vcf
added:
test-data/zika/Z52_a_annotated.tsv
test-data/zika/db/PRV.gff
removed:
test-data/zika/Z52.consensus.fa.fai
test-data/zika/Z52.consensus.qual.txt
test-data/zika/Z52_a.sorted.bam.bai
test-data/zika/Z52_a.trimmed.sorted.bam.bai
test-data/zika/Z52_b.sorted.bam.bai
test-data/zika/Z52_b.trimmed.sorted.bam.bai
test-data/zika/primer_mismatchers_indices.txt
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diff -r 0135f1d487a0 -r 72ddd32392cd ivar_filtervariants.xml
--- a/ivar_filtervariants.xml Wed Jul 13 15:19:34 2022 +0000
+++ b/ivar_filtervariants.xml Wed Jan 11 09:54:37 2023 +0000
[
@@ -1,10 +1,10 @@
-<tool id="ivar_filtervariants" name="ivar filtervariants" version="@VERSION@+galaxy0">
+<tool id="ivar_filtervariants" name="ivar filtervariants" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Filter variants across replicates or multiple samples aligned using the same reference</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[
         #for $counter, $input in enumerate($inputs):
             ln -s '$input' ./var_${counter}.tsv &&
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diff -r 0135f1d487a0 -r 72ddd32392cd macros.xml
--- a/macros.xml Wed Jul 13 15:19:34 2022 +0000
+++ b/macros.xml Wed Jan 11 09:54:37 2023 +0000
b
@@ -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>
b
diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52.consensus.fa.fai
--- a/test-data/zika/Z52.consensus.fa.fai Wed Jul 13 15:19:34 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,1 +0,0 @@
-Consensus_Z52.consensus_threshold_0_quality_20 10139 48 10139 10140
b
diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52.consensus.qual.txt
--- a/test-data/zika/Z52.consensus.qual.txt Wed Jul 13 15:19:34 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
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diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_a.sorted.bam.bai
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Binary file test-data/zika/Z52_a.sorted.bam.bai has changed
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diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_a.trimmed.sorted.bam.bai
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Binary file test-data/zika/Z52_a.trimmed.sorted.bam.bai has changed
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diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_a.tsv
--- a/test-data/zika/Z52_a.tsv Wed Jul 13 15:19:34 2022 +0000
+++ b/test-data/zika/Z52_a.tsv Wed Jan 11 09:54:37 2023 +0000
b
@@ -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
b
diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_a.vcf
--- a/test-data/zika/Z52_a.vcf Wed Jul 13 15:19:34 2022 +0000
+++ b/test-data/zika/Z52_a.vcf Wed Jan 11 09:54:37 2023 +0000
b
@@ -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
b
diff -r 0135f1d487a0 -r 72ddd32392cd 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 09:54:37 2023 +0000
b
@@ -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
b
diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_a_pass.vcf
--- a/test-data/zika/Z52_a_pass.vcf Wed Jul 13 15:19:34 2022 +0000
+++ b/test-data/zika/Z52_a_pass.vcf Wed Jan 11 09:54:37 2023 +0000
b
@@ -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
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diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_b.sorted.bam.bai
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Binary file test-data/zika/Z52_b.sorted.bam.bai has changed
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diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/Z52_b.trimmed.sorted.bam.bai
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Binary file test-data/zika/Z52_b.trimmed.sorted.bam.bai has changed
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diff -r 0135f1d487a0 -r 72ddd32392cd 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 09:54:37 2023 +0000
b
@@ -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
+###
b
diff -r 0135f1d487a0 -r 72ddd32392cd test-data/zika/primer_mismatchers_indices.txt
--- a/test-data/zika/primer_mismatchers_indices.txt Wed Jul 13 15:19:34 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,1 +0,0 @@
-400_18_out_L** 400_23_out_R 400_32_out_L
\ No newline at end of file