| Previous changeset 12:9c5754002592 (2023-02-10) Next changeset 14:e4ee04da1c19 (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_consensus.xml macros.xml test-data/zika/Z52_a.tsv test-data/zika/Z52_a_annotated.tsv |
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| diff -r 9c5754002592 -r 1069f6db0a0e ivar_consensus.xml --- a/ivar_consensus.xml Fri Feb 10 17:06:13 2023 +0000 +++ b/ivar_consensus.xml Mon Feb 13 17:30:23 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Call consensus from aligned BAM file</description> <macros> <import>macros.xml</import> @@ -13,6 +13,7 @@ -p consensus -q $min_qual -t $min_freq + -c $min_indel_freq -m $min_depth $depth_action && @@ -34,6 +35,7 @@ ]]> </help> </param> + <param name="min_indel_freq" argument="-c" type="float" min="0" max="1" value="0.8" label="Minimum indel frequency threshold" help="Same meaning as the "Minimum frequency threshold" above, but applied to indels."/> <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/> <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold"> <option value="-k">Drop from output (-k)</option> @@ -60,12 +62,14 @@ samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus [options] - There are four parameters that can be set: + There are five parameters that can be set: - **Minimum quality**: the minimum quality of a base to be considered in calculations of variant frequencies at a given position - **Minimum frequency threshold**: the minimum frequency that the most likely base must surpass to be called as the consensus base at a position. - + + - **Minimum indel frequency threshold**: has the same meaning as the previous threshold, but gets applied to indels specifically. Setting this threshold higher than the threshold applied to SNVs helps reduce indel artefacts in the generated consensus. + - **Minimum depth to call consensus**: the minimum required depth to call a consensus base - **How to represent positions with coverage less than the minimum depth threshold**: for positions for which the above minimum depth to call a consensus base is not reached, you can choose one of three different actions: |
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| diff -r 9c5754002592 -r 1069f6db0a0e macros.xml --- a/macros.xml Fri Feb 10 17:06:13 2023 +0000 +++ b/macros.xml Mon Feb 13 17:30:23 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 9c5754002592 -r 1069f6db0a0e test-data/zika/Z52_a.tsv --- a/test-data/zika/Z52_a.tsv Fri Feb 10 17:06:13 2023 +0000 +++ b/test-data/zika/Z52_a.tsv Mon Feb 13 17:30:23 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 9c5754002592 -r 1069f6db0a0e test-data/zika/Z52_a_annotated.tsv --- a/test-data/zika/Z52_a_annotated.tsv Fri Feb 10 17:06:13 2023 +0000 +++ b/test-data/zika/Z52_a_annotated.tsv Mon Feb 13 17:30:23 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 |