| Previous changeset 11:5671e1d3d5ee (2022-07-13) Next changeset 13:f0cc9cf99407 (2023-02-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324 |
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modified:
ivar_trim.xml macros.xml test-data/zika/Z52_a.tsv test-data/zika/Z52_a.vcf test-data/zika/Z52_a_pass.vcf |
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added:
test-data/zika/Z52_a_annotated.tsv test-data/zika/db/PRV.gff |
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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 5671e1d3d5ee -r e3bb03cf207a ivar_trim.xml --- a/ivar_trim.xml Wed Jul 13 15:18:33 2022 +0000 +++ b/ivar_trim.xml Wed Jan 11 09:55:20 2023 +0000 |
| [ |
| @@ -1,13 +1,10 @@ -<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy4" profile="21.01"> +<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@"> <description>Trim reads in aligned BAM</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="3.8.1">python</requirement> - <requirement type="package" version="1.15">samtools</requirement> - </expand> - <expand macro="version_command" /> + <expand macro="requirements"/> + <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ #if $primer.source == 'history' cp '$primer.input_bed' bed.bed && @@ -114,7 +111,18 @@ <param name="input_bed" value="zika/db/zika_primers.bed" /> </conditional> <param name="input_bam" value="zika/Z52_b.sorted.bam" /> - <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/> + <output name="output_bam" ftype="bam"> + <assert_contents> + <has_size value="4023965" delta="1000"/> + </assert_contents> + </output> + <assert_stdout> + <has_text text="Found 68 primers in BED file"/> + <has_text text="Using Region: PRV"/> + <has_text text="Found 40964 mapped reads"/> + <has_text text="reads were quality trimmed below the minimum length of 30 bp and were not written to file"/> + <has_text text="reads that started outside of primer regions were not written to file"/> + </assert_stdout> </test> <test> <conditional name="primer"> |
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| diff -r 5671e1d3d5ee -r e3bb03cf207a macros.xml --- a/macros.xml Wed Jul 13 15:18:33 2022 +0000 +++ b/macros.xml Wed Jan 11 09:55:20 2023 +0000 |
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| @@ -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> |
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| diff -r 5671e1d3d5ee -r e3bb03cf207a test-data/zika/Z52.consensus.fa.fai --- a/test-data/zika/Z52.consensus.fa.fai Wed Jul 13 15:18:33 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -Consensus_Z52.consensus_threshold_0_quality_20 10139 48 10139 10140 |
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| diff -r 5671e1d3d5ee -r e3bb03cf207a test-data/zika/Z52.consensus.qual.txt --- a/test-data/zika/Z52.consensus.qual.txt Wed Jul 13 15:18:33 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1 +0,0 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| diff -r 5671e1d3d5ee -r e3bb03cf207a 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 5671e1d3d5ee -r e3bb03cf207a 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 5671e1d3d5ee -r e3bb03cf207a test-data/zika/Z52_a.tsv --- a/test-data/zika/Z52_a.tsv Wed Jul 13 15:18:33 2022 +0000 +++ b/test-data/zika/Z52_a.tsv Wed Jan 11 09:55:20 2023 +0000 |
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| @@ -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 |
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| diff -r 5671e1d3d5ee -r e3bb03cf207a test-data/zika/Z52_a.vcf --- a/test-data/zika/Z52_a.vcf Wed Jul 13 15:18:33 2022 +0000 +++ b/test-data/zika/Z52_a.vcf Wed Jan 11 09:55:20 2023 +0000 |
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| @@ -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 |
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| diff -r 5671e1d3d5ee -r e3bb03cf207a 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 09:55:20 2023 +0000 |
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| @@ -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 |
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| diff -r 5671e1d3d5ee -r e3bb03cf207a test-data/zika/Z52_a_pass.vcf --- a/test-data/zika/Z52_a_pass.vcf Wed Jul 13 15:18:33 2022 +0000 +++ b/test-data/zika/Z52_a_pass.vcf Wed Jan 11 09:55:20 2023 +0000 |
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| @@ -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 5671e1d3d5ee -r e3bb03cf207a 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 5671e1d3d5ee -r e3bb03cf207a 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 5671e1d3d5ee -r e3bb03cf207a 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 09:55:20 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 5671e1d3d5ee -r e3bb03cf207a test-data/zika/primer_mismatchers_indices.txt --- a/test-data/zika/primer_mismatchers_indices.txt Wed Jul 13 15:18:33 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 |