| Previous changeset 12:31ea13dfe5e6 (2022-08-19) Next changeset 14:aaff91a85471 (2022-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49 |
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modified:
bcftools_mpileup.xml macros.xml test-data/summary.pdf |
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added:
test-data/mpileup.AD.vcf |
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| diff -r 31ea13dfe5e6 -r 37757ffb4c5f bcftools_mpileup.xml --- a/bcftools_mpileup.xml Fri Aug 19 19:51:22 2022 +0000 +++ b/bcftools_mpileup.xml Tue Sep 20 12:50:07 2022 +0000 |
| [ |
| b'@@ -1,5 +1,5 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">\n+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>\n <macros>\n <token name="@EXECUTABLE@">mpileup</token>\n@@ -97,14 +97,32 @@\n #end if\n #end if\n \n+#if $section.ambig_reads\n+ --ambig-reads $section.ambig_reads\n+#end if\n+\n+#if $section.indel_bias\n+ --indel-bias $section.indel_bias\n+#end if\n+\n+#if $section.indel_size\n+ --indel-size $section.indel_size\n+#end if\n+\n ## Filter section\n #set $section = $sec_filtering\n #if str( $section.filter_by_flags.filter_flags ) == "filter":\n- #if $section.filter_by_flags.require_flags:\n- --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(\',\')])}\n+ #if $section.filter_by_flags.skip_all_set:\n+ --skip-all-set ${sum([int(flag) for flag in str($section.filter_by_flags.skip_all_set).split(\',\')])}\n+ #end if\n+ #if $section.filter_by_flags.skip_any_set:\n+ --skip-any-set ${sum([int(flag) for flag in str($section.filter_by_flags.skip_any_set).split(\',\')])}\n #end if\n- #if $section.filter_by_flags.exclude_flags:\n- --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(\',\')])}\n+ #if $section.filter_by_flags.skip_all_unset:\n+ --skip-all-unset ${sum([int(flag) for flag in str($section.filter_by_flags.skip_all_unset).split(\',\')])}\n+ #end if\n+ #if $section.filter_by_flags.skip_any_unset:\n+ --skip-any-unset ${sum([int(flag) for flag in str($section.filter_by_flags.skip_any_unset).split(\',\')])}\n #end if\n #end if\n -d "${section.max_reads_per_bam}"\n@@ -140,9 +158,7 @@\n #set $section = $sec_restrict\n @REGIONS@\n @TARGETS@\n-\n @THREADS@\n-\n @OUTPUT_TYPE@\n \n ## Primary Input/Outputs\n@@ -221,6 +237,13 @@\n </when>\n <when value="do_not_perform_indel_calling" />\n </conditional>\n+ <param argument="--ambig-reads" type="select" optional="true" label="Ambiguous indel reads" help="What to do with ambiguous indel reads that do not span an entire short tandem repeat region: discard ambiguous reads from calling and do not increment high-quality AD depth counters (drop), exclude from calling but increment AD counters proportionally (incAD), exclude from calling and increment the first value of the AD counter (incAD0) ">\n+ <option value="drop">Drop</option>\n+ <option value="incAD">IncAD</option>\n+ <option value="incAD0">IncAD0</option>\n+ </param>\n+ <param argument="--indel-bias" type="float" min="0" value="" optional="true" label="Indel bias" help="Skews the indel scores up or down, trading recall (low false-negative) vs precision (low false-positive) [1.0]. In Bcftools 1.12 and earlier this parameter didn\xe2\x80\x99t exist, but had an implied value of 1.0. If you are planning to do heavy filtering of variants, selecting the best quality ones only (favouring precision over recall), it is advisable to set this lower (such as 0.75) while higher depth samples or where you favour recall rates over precision may work better with a higher value such as 2.0" />\n+ <param argument="--indel-size" type="integer" min="0" value="" optional="true" label="Indel size" help="Indel window size to use when assessing the quality of candidate indels. Note that although the window size approximately corresponds to the maximum indel size considered, it is not an exact threshold. Default: 110" />\n </section>\n \n <section name="sec_filtering" expanded="false" title="Input Filtering Options">\n@@ -233,10 +256,16 @@\n <option value="filter">Filter by flags to exclude or require</option>\n '..b' +332,7 @@\n </section>\n \n <section name="sec_output_options" expanded="false" title="Output options">\n- <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags">\n+ <expand macro="macro_output_tags">\n <option value="DP">DP (Number of high-quality bases)</option>\n <option value="AD">AD (Allelic depth)</option>\n <option value="ADF">ADF (Allelic depth on the forward strand)</option>\n@@ -313,10 +342,11 @@\n <option value="INFO/ADR">INFO/ADR (Allelic depth on the reverse strand)</option>\n <option value="SP">SP (Phred-scaled strand bias P-value)</option>\n <option value="DV">DV (Number of high-quality non-reference bases)</option>\n+ <option value="QS">QS (Allele phred-score quality sum)</option>\n <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option>\n <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>\n <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option>\n- </param>\n+ </expand>\n <param name="gvcf" type="text" value="" label="gVCF blocks of homozygous REF calls">\n <help>\n output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the list of integers. For example, passing 5,15 will group sites into two types of gVCF blocks, the first with minimum per-sample DP from the interval [5,15) and the latter with minimum depth 15 or more. In this example, sites with minimum per-sample depth less than 5 will be printed as separate records, outside of gVCF blocks. \n@@ -451,15 +481,45 @@\n </conditional>\n </section>\n <param name="filter_flags" value="filter" />\n- <param name="exclude_flags" value="4,16" />\n+ <param name="skip_all_set" value="4,16" /> \n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n <has_text text="mpileup" />\n <has_text text="HG00100" />\n- <has_text_matching expression="17\\t1050\\t.\\tA\\t...\\t0\\t.\\tDP=12;" />\n+ <has_text_matching expression="17\\t1050\\t.\\tA\\t" />\n </assert_contents>\n </output>\n+ <assert_command>\n+ <has_text text="--skip-all-set" />\n+ </assert_command>\n+ </test>\n+ <!-- Test indel options-->\n+ <test>\n+ <param name="input_number" value="single" />\n+ <param name="input_bam" ftype="bam" value="mpileup.1.bam" />\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />\n+ <section name="sec_indel">\n+ <param name="ambig_reads" value="drop"/>\n+ <param name="indel_bias" value="1"/>\n+ <param name="indel_size" value="110"/>\n+ </section>\n+ <param name="output_type" value="v" />\n+ <output name="output_file">\n+ <assert_contents>\n+ <has_text text="mpileup" />\n+ <has_text text="HG00100" />\n+ <has_text_matching expression="17\\t1\\t.\\tA\\t...\\t0\\t.\\tDP=5;" />\n+ <has_text_matching expression="17\\t100\\t.\\tC\\t...\\t0\\t.\\tDP=9;" />\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="--ambig-reads" />\n+ <has_text text="--indel-bias" />\n+ <has_text text="--indel-size" />\n+ </assert_command>\n+ \n </test>\n </tests>\n <help><![CDATA[\n' |
| b |
| diff -r 31ea13dfe5e6 -r 37757ffb4c5f macros.xml --- a/macros.xml Fri Aug 19 19:51:22 2022 +0000 +++ b/macros.xml Tue Sep 20 12:50:07 2022 +0000 |
| [ |
| @@ -1,5 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">1.10</token> + <token name="@TOOL_VERSION@">1.15.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">bcftools</xref> @@ -8,15 +10,15 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement> - <requirement type="package" version="1.10">htslib</requirement> + <requirement type="package" version="1.15.1">htslib</requirement> <yield /> </requirements> </xml> <xml name="samtools_requirement"> - <requirement type="package" version="1.10">samtools</requirement> + <requirement type="package" version="1.15.1">samtools</requirement> </xml> <xml name="matplotlib_requirement"> - <requirement type="package" version="3.4.3">matplotlib</requirement> + <requirement type="package" version="3.5.3">matplotlib</requirement> </xml> <xml name="version_command"> <version_command>bcftools 2>&1 | grep 'Version:'</version_command> @@ -39,6 +41,10 @@ ]]> </token> <xml name="macro_input"> + <!-- + REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files + <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" /> + --> <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" /> </xml> <token name="@PREPARE_INPUT_FILE@"> @@ -48,6 +54,7 @@ #if $input_file.is_of_type('vcf') bgzip -c '$input_file' > $input_vcf && bcftools index $input_vcf && +##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') #elif $input_file.is_of_type('vcf_bgzip') ln -s '$input_file' $input_vcf && #if $input_file.metadata.tabix_index: @@ -71,6 +78,10 @@ </token> <xml name="macro_inputs"> + <!-- + REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files + <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" /> + --> <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" /> </xml> <token name="@PREPARE_INPUT_FILES@"> @@ -83,7 +94,8 @@ #if $input_file.is_of_type('vcf') bgzip -c '$input_file' > $input_vcf && bcftools index $input_vcf && - #elif $input_file.is_of_type('vcf_bgzip') + ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605 + #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') ln -s '$input_file' $input_vcf && #if $input_file.metadata.tabix_index: ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi && @@ -318,6 +330,11 @@ <yield /> </when> </conditional> + <param argument="--@TYPE@s-overlap" type="select" optional="true" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)"> + <option value="0">0: POS in the region</option> + <option value="1">1: Record overlaps</option> + <option value="2">2: Variant overlaps</option> + </param> </xml> <token name="@PARSE_INTERVALS@"> @@ -337,6 +354,28 @@ ]]> </token> + <token name="@MASK@"> +<![CDATA[ +#if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter + #if $section.conditional_soft_filter.masks.masks_src == 'regions': + #set $intervals = $section.conditional_soft_filter.masks.masks + @PARSE_INTERVALS@ + --mask '$intervals_spec' + #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file' and $section.conditional_soft_filter.masks.masks_file: + #if $masks_path is not None: + --mask-file '$masks_path' + #else: + --mask-file '$section.conditional_soft_filter.masks.masks_file' + #end if + #end if + #if $section.conditional_soft_filter.masks_overlap + --mask-overlap $section.conditional_soft_filter.masks_overlap + #end if +#end if + +]]> + </token> + <token name="@REGIONS@"> <![CDATA[ #if $section.regions.regions_src == 'regions': @@ -350,6 +389,10 @@ --regions-file '$section.regions.regions_file' #end if #end if +#if $section.regions_overlap + --regions-overlap $section.regions_overlap +#end if + ]]> </token> @@ -364,6 +407,9 @@ #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" #end if +#if $section.targets_overlap + --targets-overlap $section.targets_overlap +#end if ]]> </token> @@ -410,8 +456,8 @@ <xml name="macro_samples"> <param argument="--samples" type="text" value="" optional="true" label="Samples" - help="Comma separated list of samples to annotate (or exclude)"> - <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> + help="Comma-separated list of samples to annotate (or exclude) or - to include all samples"> + <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator> </param> <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" /> @@ -476,7 +522,7 @@ <xml name="macro_columns"> <param name="columns" type="text" value="" optional="true" label="Columns" help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> - <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> + <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> </param> </xml> <token name="@COLUMNS@"> @@ -496,7 +542,18 @@ ${section.vcf_ids} </token> +<xml name="macro_output_tags"> + <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate"> + <yield /> + </param> +</xml> + +<xml name="macro_overlap" token_argument="" token_label=""> +</xml> + + <token name="@OUTPUT_HELP@"> + <![CDATA[ Output Type ----------- |
| b |
| diff -r 31ea13dfe5e6 -r 37757ffb4c5f test-data/mpileup.AD.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.AD.vcf Tue Sep 20 12:50:07 2022 +0000 |
| b |
| b'@@ -0,0 +1,4131 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##bcftoolsVersion=1.11-21-g0987715+htslib-1.11-3-g450c912\n+##bcftoolsCommand=mpileup -O v -a AD,DP,INFO/ADR,INFO/ADF,DP4,INFO/DPR -f xxx//mpileup.ref.fa -b xxx//bamlist.txt\n+##reference=file://mpileup.ref.fa\n+##contig=<ID=17,length=4200>\n+##ALT=<ID=*,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">\n+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n+##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">\n+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">\n+##INFO=<ID=ADF,Number=R,Type=Integer,Description="Total allelic depths on the forward strand (high-quality bases)">\n+##INFO=<ID=ADR,Number=R,Type=Integer,Description="Total allelic depths on the reverse strand (high-quality 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