| Previous changeset 11:38b91a3190cd (2023-01-11) Next changeset 13:3b6a16d82c1b (2023-03-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73 |
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modified:
ivar_variants.xml macros.xml test-data/zika/Z52_a.tsv test-data/zika/Z52_a_annotated.tsv |
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| diff -r 38b91a3190cd -r ed28dd32141c ivar_variants.xml --- a/ivar_variants.xml Wed Jan 11 09:53:09 2023 +0000 +++ b/ivar_variants.xml Mon Feb 13 17:29:40 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> +<tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Call variants from aligned BAM file</description> <macros> <import>macros.xml</import> @@ -27,7 +27,7 @@ <inputs> <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> <param name="ref" type="data" format="fasta" label="Reference"/> - <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/> + <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/> <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> <conditional name="output_format"> <param name="choice" type="select" label="Output format"> @@ -51,7 +51,7 @@ <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}"> <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter> <actions> - <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA"/> + <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA,POS_AA"/> </actions> </data> <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> |
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| diff -r 38b91a3190cd -r ed28dd32141c macros.xml --- a/macros.xml Wed Jan 11 09:53:09 2023 +0000 +++ b/macros.xml Mon Feb 13 17:29:40 2023 +0000 |
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| @@ -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> |
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| diff -r 38b91a3190cd -r ed28dd32141c test-data/zika/Z52_a.tsv --- a/test-data/zika/Z52_a.tsv Wed Jan 11 09:53:09 2023 +0000 +++ b/test-data/zika/Z52_a.tsv Mon Feb 13 17:29:40 2023 +0000 |
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| @@ -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 |
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| diff -r 38b91a3190cd -r ed28dd32141c test-data/zika/Z52_a_annotated.tsv --- a/test-data/zika/Z52_a_annotated.tsv Wed Jan 11 09:53:09 2023 +0000 +++ b/test-data/zika/Z52_a_annotated.tsv Mon Feb 13 17:29:40 2023 +0000 |
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| @@ -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 |