| Previous changeset 10:ee29337f905c (2022-07-13) Next changeset 12:8c05afb547fa (2023-02-13) |
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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_removereads.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 ee29337f905c -r 7f1cfa4c0e32 ivar_removereads.xml --- a/ivar_removereads.xml Wed Jul 13 15:20:33 2022 +0000 +++ b/ivar_removereads.xml Wed Jan 11 09:56:04 2023 +0000 |
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| @@ -1,12 +1,10 @@ -<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy3" profile="21.01"> +<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> <description>Remove reads from trimmed BAM file</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="3.8.1">python</requirement> - </expand> - <expand macro="version_command" /> + <expand macro="requirements"/> + <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ cp '$input_bed' binding_sites.bed && python '$__tool_directory__/sanitize_bed.py' binding_sites.bed && @@ -31,10 +29,10 @@ <inputs> <param name="input_bam" argument="-i" type="data" format="bam" label="Bam input" - help="BAM dataset, preprocessed with ivar trim, to remove reads from" /> + help="BAM dataset, preprocessed with ivar trim, to remove reads from"/> <param name="variants_tsv" type="data" format="tabular" label="Variants input" - help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS." /> + help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS."/> <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information" help="The same six-column BED dataset that served as input to ivar trim"/> <conditional name="amplicons"> @@ -59,19 +57,27 @@ <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/> <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/> <conditional name="amplicons"> - <param name="computed" value="no" /> + <param name="computed" value="no"/> <param name="amplicon_info" value="zika/db/pair_information.tsv"/> </conditional> - <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" /> + <output name="output_bam" ftype="bam"> + <assert_contents> + <has_size value="3185672" delta="1000"/> + </assert_contents> + </output> </test> <test> <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/> <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/> <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/> <conditional name="amplicons"> - <param name="computed" value="yes" /> + <param name="computed" value="yes"/> </conditional> - <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" /> + <output name="output_bam" ftype="bam"> + <assert_contents> + <has_size value="3185672" delta="1000"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ |
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| diff -r ee29337f905c -r 7f1cfa4c0e32 macros.xml --- a/macros.xml Wed Jul 13 15:20:33 2022 +0000 +++ b/macros.xml Wed Jan 11 09:56:04 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 ee29337f905c -r 7f1cfa4c0e32 test-data/zika/Z52.consensus.fa.fai --- a/test-data/zika/Z52.consensus.fa.fai Wed Jul 13 15:20:33 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 ee29337f905c -r 7f1cfa4c0e32 test-data/zika/Z52.consensus.qual.txt --- a/test-data/zika/Z52.consensus.qual.txt Wed Jul 13 15:20:33 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 ee29337f905c -r 7f1cfa4c0e32 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 ee29337f905c -r 7f1cfa4c0e32 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 ee29337f905c -r 7f1cfa4c0e32 test-data/zika/Z52_a.tsv --- a/test-data/zika/Z52_a.tsv Wed Jul 13 15:20:33 2022 +0000 +++ b/test-data/zika/Z52_a.tsv Wed Jan 11 09:56:04 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 ee29337f905c -r 7f1cfa4c0e32 test-data/zika/Z52_a.vcf --- a/test-data/zika/Z52_a.vcf Wed Jul 13 15:20:33 2022 +0000 +++ b/test-data/zika/Z52_a.vcf Wed Jan 11 09:56:04 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 ee29337f905c -r 7f1cfa4c0e32 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 09:56:04 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 ee29337f905c -r 7f1cfa4c0e32 test-data/zika/Z52_a_pass.vcf --- a/test-data/zika/Z52_a_pass.vcf Wed Jul 13 15:20:33 2022 +0000 +++ b/test-data/zika/Z52_a_pass.vcf Wed Jan 11 09:56:04 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 ee29337f905c -r 7f1cfa4c0e32 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 ee29337f905c -r 7f1cfa4c0e32 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 ee29337f905c -r 7f1cfa4c0e32 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 09:56:04 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 ee29337f905c -r 7f1cfa4c0e32 test-data/zika/primer_mismatchers_indices.txt --- a/test-data/zika/primer_mismatchers_indices.txt Wed Jul 13 15:20:33 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 |