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

Changeset 12:8f8df367470d (2023-02-13)
Previous changeset 11:72ddd32392cd (2023-01-11) Next changeset 13:9537184d421f (2023-03-25)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
modified:
ivar_filtervariants.xml
macros.xml
test-data/zika/Z52_a.tsv
test-data/zika/Z52_a_annotated.tsv
b
diff -r 72ddd32392cd -r 8f8df367470d ivar_filtervariants.xml
--- a/ivar_filtervariants.xml Wed Jan 11 09:54:37 2023 +0000
+++ b/ivar_filtervariants.xml Mon Feb 13 17:28:58 2023 +0000
b
@@ -1,4 +1,4 @@
-<tool id="ivar_filtervariants" name="ivar filtervariants" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="ivar_filtervariants" name="ivar filtervariants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Filter variants across replicates or multiple samples aligned using the same reference</description>
         <macros>
         <import>macros.xml</import>
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diff -r 72ddd32392cd -r 8f8df367470d macros.xml
--- a/macros.xml Wed Jan 11 09:54:37 2023 +0000
+++ b/macros.xml Mon Feb 13 17:28:58 2023 +0000
b
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@TOOL_VERSION@">1.3.1</token>
+  <token name="@TOOL_VERSION@">1.3.2</token>
   <token name="@PROFILE@">21.01</token>
   <xml name="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>
+      <requirement type="package" version="1.16.1">samtools</requirement>
       <yield/>
   </requirements>
   </xml>
b
diff -r 72ddd32392cd -r 8f8df367470d test-data/zika/Z52_a.tsv
--- a/test-data/zika/Z52_a.tsv Wed Jan 11 09:54:37 2023 +0000
+++ b/test-data/zika/Z52_a.tsv Mon Feb 13 17:28:58 2023 +0000
b
@@ -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 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 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
-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
+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 POS_AA
+PRV 350 A T 101 101 36 5 5 35 0.0471698 106 0.0304989 FALSE NA 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 NA
+PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE NA 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 NA
+PRV 2702 A G 31 31 36 1 1 23 0.03125 32 0.507937 FALSE NA 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 NA
+PRV 2922 C T 264 0 36 11 0 36 0.04 275 0.000440953 TRUE NA 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 NA
+PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE NA 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 NA
+PRV 5680 C T 27 10 44 8 3 46 0.228571 35 0.000596701 TRUE NA 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 NA
+PRV 6201 A G 10 0 35 2 0 38 0.166667 12 0.26087 FALSE NA 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 NA
+PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE NA 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 NA
b
diff -r 72ddd32392cd -r 8f8df367470d test-data/zika/Z52_a_annotated.tsv
--- a/test-data/zika/Z52_a_annotated.tsv Wed Jan 11 09:54:37 2023 +0000
+++ b/test-data/zika/Z52_a_annotated.tsv Mon Feb 13 17:28:58 2023 +0000
b
@@ -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 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
+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 POS_AA
+PRV 350 A T 101 101 36 5 5 35 0.0471698 106 0.0304989 FALSE POLY:cds-YP_002790881.1 AAA K TAA * 82
+PRV 722 C +A 280 234 36 9 0 20 0.0319149 282 0.0349042 FALSE NA NA NA NA NA NA
+PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE POLY:cds-YP_002790881.1 CTG L TTG L 526
+PRV 1965 T G 302 113 37 63 25 37 0.172603 365 4.41891e-21 TRUE POLY:cds-YP_002790881.1 GTT V GGT G 620
+PRV 2702 A G 31 31 36 1 1 23 0.03125 32 0.507937 FALSE POLY:cds-YP_002790881.1 AGA R GGA G 866
+PRV 2781 T G 354 70 37 48 8 36 0.117647 408 4.33605e-16 TRUE POLY:cds-YP_002790881.1 GTG V GGG G 892
+PRV 2922 C T 264 0 36 11 0 36 0.04 275 0.000440953 TRUE POLY:cds-YP_002790881.1 ACT T ATT I 939
+PRV 3148 Y T 0 0 0 1324 264 36 0.77563 1707 0 TRUE POLY:cds-YP_002790881.1 GAY X GAT D 1014
+PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE POLY:cds-YP_002790881.1 GAY X GAC D 1014
+PRV 3295 A G 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE POLY:cds-YP_002790881.1 GCA A GCG A 1063
+PRV 5680 C T 27 10 44 8 3 46 0.228571 35 0.000596701 TRUE POLY:cds-YP_002790881.1 TTC F TTT F 1858
+PRV 5723 T G 31 31 35 1 1 21 0.03125 32 0.507937 FALSE POLY:cds-YP_002790881.1 TGA * GGA G 1873
+PRV 6201 A G 10 0 35 2 0 38 0.166667 12 0.26087 FALSE POLY:cds-YP_002790881.1 GAA E GGA G 2032
+PRV 6211 T C 8 0 36 1 0 35 0.111111 9 0.5 FALSE POLY:cds-YP_002790881.1 TGT C TGC C 2035
+PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE POLY:cds-YP_002790881.1 CAG Q TAG * 2604
+PRV 9713 C T 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE POLY:cds-YP_002790881.1 CTT L TTT F 3203