| Previous changeset 15:33bd9301568c (2022-07-23) Next changeset 17:6ea7170a016d (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_filter.xml macros.xml test-data/summary.pdf |
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added:
test-data/mpileup.AD.vcf |
| b |
| diff -r 33bd9301568c -r e7452697afd9 bcftools_filter.xml --- a/bcftools_filter.xml Sat Jul 23 13:39:59 2022 +0000 +++ b/bcftools_filter.xml Tue Sep 20 13:17:14 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@">\n+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>Apply fixed-threshold filters</description>\n <macros>\n <token name="@EXECUTABLE@">filter</token>\n@@ -29,8 +29,9 @@\n #set $mode = str($section.mode).replace(\',\',\'\')\n --mode \'$mode\'\n #end if\n-#if $section.soft_filter:\n- --soft-filter "${section.soft_filter}"\n+#if $section.conditional_soft_filter.selector == \'enabled\':\n+ --soft-filter \'${section.conditional_soft_filter.soft_filter}\'\n+ @MASK@\n #end if\n #if $section.select_set_GTs:\n --set-GTs "${section.select_set_GTs}"\n@@ -70,11 +71,22 @@\n <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option>\n <option value="x">(x) resets filters of sites which pass to "PASS"</option>\n </param>\n- <param name="soft_filter" type="text" value="" label="Soft Filter" optional="true">\n- <help><![CDATA[ (-s) \n- Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").\n- ]]></help>\n- </param>\n+ <conditional name="conditional_soft_filter">\n+ <param name="selector" type="select" label="Perform soft filtering">\n+ <option value="disabled">Disabled</option>\n+ <option value="enabled">Enabled</option>\n+ </param>\n+ <when value="disabled"/>\n+ <when value="enabled">\n+ <param argument="--soft-filter" type="text" value="" label="Soft Filter" optional="true">\n+ <help><![CDATA[ (-s) \n+ Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").\n+ ]]></help>\n+ </param>\n+ <expand macro="macro_restrict" type="mask" label_type="Mask"/>\n+ </when>\n+ </conditional>\n+\n <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)">\n <option value=".">to missing (.)</option>\n <option value="0">to REF (0)</option>\n@@ -107,9 +119,9 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="Modified" />\n+ <has_text text="genotypes" />\n <has_text text="AN=2;AC=1" />\n- <has_text_matching expression="TAAAA\\tTA,T\\t61.5\\tModified" />\n+ <has_text_matching expression="TAAAA\\tTA,T\\t61.5\\tPASS" />\n </assert_contents>\n </output>\n </test>\n@@ -128,7 +140,12 @@\n <test>\n <param name="input_file" ftype="vcf" value="filter.3.vcf" />\n <param name="exclude" value="INFO/DP=19" />\n- <param name="soft_filter" value="XX" />\n+ <section name="sec_filter">\n+ <conditional name="conditional_soft_filter">\n+ <param name="selector" value="enabled"/>\n+ <param name="soft_filter" value="XX" />\n+ </conditional>\n+ </section>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n@@ -140,12 +157,17 @@\n <test>\n <param name="input_file" ftype="vcf" value="filter.3.vcf" />\n <param name="exclude" value="INFO/DP=19" />\n- <param name="soft_filter" value="XX" />\n- <param name="mode" value="+" />\n+ <section name="sec_filter">\n+ <conditional name="conditional_soft_f'..b'm name="input_file" ftype="vcf" value="filter.3.vcf" />\n <param name="exclude" value="INFO/DP=19" />\n- <param name="soft_filter" value="XX" />\n- <param name="mode" value="x" />\n+ <section name="sec_filter">\n+ <conditional name="conditional_soft_filter">\n+ <param name="selector" value="enabled"/>\n+ <param name="soft_filter" value="XX" />\n+ <param name="mode" value="+" />\n+ </conditional>\n+ </section>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n <has_text_matching expression="\\tXX\\tDP=19" />\n- <has_text_matching expression="\\tPASS\\tAO" />\n+ <has_text_matching expression="\\tq20\\tAO=52101" />\n </assert_contents>\n </output>\n </test>\n <test>\n <param name="input_file" ftype="vcf" value="filter.3.vcf" />\n <param name="exclude" value="INFO/DP=19" />\n- <param name="soft_filter" value="XX" />\n- <param name="mode" value="+,x" />\n+ <section name="sec_filter">\n+ <conditional name="conditional_soft_filter">\n+ <param name="selector" value="enabled"/>\n+ <param name="soft_filter" value="XX" />\n+ <param name="mode" value="+" />\n+ </conditional>\n+ </section>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text_matching expression="\\tq20;XX\\tDP=19" />\n- <has_text_matching expression="\\tPASS\\tAO" />\n+ <has_text_matching expression="\\t238\\tXX\\tDP=19" />\n+ <has_text_matching expression="\\t238\\tq20\\tAO" />\n </assert_contents>\n </output>\n </test>\n@@ -198,6 +230,48 @@\n </assert_contents>\n </output>\n </test>\n+ <!-- Test region overlap -->\n+ <test>\n+ <param name="input_file" ftype="vcf" value="filter.2.vcf" />\n+ <param name="include" value="FMT/GT="0/0" && AC[*]=2" />\n+ <param name="output_type" value="v" />\n+ <section name="sec_restrict">\n+ <param name="regions_overlap" value="1"/>\n+ </section>\n+ <output name="output_file">\n+ <assert_contents>\n+ <has_text text="AN=4;AC=2" />\n+ <not_has_text text="AN=4;AC=0" />\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="--regions-overlap" />\n+ </assert_command>\n+ </test>\n+ <!-- Test mask options-->\n+ <test>\n+ <param name="input_file" ftype="vcf" value="filter.3.vcf" />\n+ <param name="exclude" value="INFO/DP=19" />\n+ <section name="sec_filter">\n+ <param name="mode" value="+,x" />\n+ <conditional name="conditional_soft_filter">\n+ <param name="selector" value="enabled"/>\n+ <param name="soft_filter" value="XX" />\n+ <param name="masks_overlap" value="1"/>\n+ </conditional>\n+ </section>\n+\n+ <param name="output_type" value="v" />\n+ <output name="output_file">\n+ <assert_contents>\n+ <has_text_matching expression="\\tq20;XX\\tDP=19" />\n+ <has_text_matching expression="\\tPASS\\tAO" />\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="--mask-overlap" />\n+ </assert_command>\n+ </test>\n </tests>\n <help><![CDATA[\n =====================================\n' |
| b |
| diff -r 33bd9301568c -r e7452697afd9 macros.xml --- a/macros.xml Sat Jul 23 13:39:59 2022 +0000 +++ b/macros.xml Tue Sep 20 13:17:14 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 33bd9301568c -r e7452697afd9 test-data/mpileup.AD.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.AD.vcf Tue Sep 20 13:17:14 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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