Mercurial > repos > jjohnson > bcftools_plugin_missing2ref
diff macros.xml @ 0:ff65d6e0809b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
| author | jjohnson |
|---|---|
| date | Sat, 25 Jun 2016 20:51:04 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jun 25 20:51:04 2016 -0400 @@ -0,0 +1,674 @@ + +<macros> + <token name="@VERSION@">1.3</token> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.3">bcftools</requirement> + <!-- conda dependency --> + <requirement type="package" version="1.3">htslib</requirement> + <requirement type="package" version="0.2.6">tabix</requirement> + <requirement type="package" version="1.2">samtools</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>bcftools 2>&1 | grep 'Version:'</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <yield /> + </citations> + </xml> + <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token> + <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token> + <token name="@THREADS@"> + --threads \${GALAXY_SLOTS:-4} + </token> + <token name="@PREPARE_ENV@"> +<![CDATA[ +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; +]]> + </token> + <xml name="macro_input"> + <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" /> + </xml> + <token name="@PREPARE_INPUT_FILE@"> +<![CDATA[ +## May need to symlink input if there is an associated +#set $input_vcf = 'input.vcf.gz' +#if $input_file.datatype.file_ext == 'vcf' + bgzip -c "$input_file" > $input_vcf && + bcftools index $input_vcf && +#elif $input_file.datatype.file_ext == 'vcf_bgzip' + ln -s "$input_file" $input_vcf +#elif $input_file.datatype.file_ext == 'bcf' + #set $input_vcf = 'input.bcf' + ln -s "$input_file" $input_vcf && + #if $input_file.metadata.bcf_index: + ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && + #else + bcftools index $input_vcf && + #end if +#elif $input_file.datatype.file_ext == 'bcf_bgzip' + ln -s "$input_file" $input_vcf +#end if +]]> + </token> + <token name="@INPUT_FILE@"> +$input_vcf + </token> + + <xml name="macro_inputs"> + <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" /> + </xml> + <token name="@PREPARE_INPUT_FILES@"> +<![CDATA[ +## May need to symlink input if there is an associated +#set $input_vcfs = [] +#set $vcfs_list_file = 'vcfs_list' +#for (i,input_file) in enumerate($input_files): + #set $input_vcf = 'input' + str($i) + '.vcf.gz' + echo '$input_vcf' >> $vcfs_list_file && + #if $input_file.datatype.file_ext == 'vcf' + bgzip -c "$input_file" > $input_vcf && + bcftools index $input_vcf && + #elif $input_file.datatype.file_ext == 'vcf_bgz' + ln -s "$input_file" $input_vcf + #elif $input_file.datatype.file_ext == 'bcf' + #set $input_vcf = 'input' + str($i) + '.bcf.gz' + ## bgzip -c "$input_file" > $input_vcf && + ln -s "$input_file" $input_vcf && + #if $input_file.metadata.bcf_index: + ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && + #else + bcftools index $input_vcf && + #end if + #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' + ln -s "$input_file" $input_vcf && + #end if + $input_vcfs.append($input_vcf) +#end for +]]> + </token> + <token name="@INPUT_FILES@"> +#echo ' '.join($input_vcfs)# + </token> + <token name="@INPUT_LIST_FILE@"> +$vcfs_list_file + </token> + + <xml name="macro_fasta_ref"> + <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" /> + </xml> + <token name="@PREPARE_FASTA_REF@"> +<![CDATA[ +#set $input_fa_ref = None +#if 'fasta_ref' in $section and $section.fasta_ref: + #set $input_fa_ref = 'ref.fa' + ln -s $section.fasta_ref $input_fa_ref && + samtools faidx $input_fa_ref && +#end if +]]> + </token> + <token name="@FASTA_REF@"> +#if $input_fa_ref is not None: + --fasta-ref "$input_fa_ref" +#elif 'fasta_ref' in $section and $section.fasta_ref: + --fasta-ref "${section.fasta_ref}" +#end if + </token> + + <xml name="macro_ref_fasta"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Select reference genome"> + <options from_data_table="fasta_indexes"> + <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> <!-- FIX ME!!!! --> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + </xml> + + + <xml name="macro_AF_file"> + <param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" /> + </xml> + <!-- This may need to bgzip and tabix the file --> + <token name="@PREPARE_AF_FILE@"> +<![CDATA[ +#if 'AF_file' in $section and $section.AF_file: +#pass +#end if +]]> + </token> + <token name="@AF_FILE@"> +#if 'AF_file' in $section and $section.AF_file: + --AF-file "${section.AF_file}" +#end if + </token> + + <xml name="macro_estimate_AF"> + <param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" help="calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> + </xml> + <token name="@ESTIMATE_AF@"> +#if 'estimate_AF' in $section and $section.estimate_AF: + --estimate-AF "${section.estimate_AF}" +#end if + </token> + + <xml name="macro_exons_file"> + <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" /> + </xml> + <token name="@PREPARE_EXONS_FILE@"> +<![CDATA[ +#set $exons_path = None +#if 'exons_file' in $section and $section.exons_file: + #set $exons_path = 'exons_file.tab.gz' + bgzip -c "$section.exons_file" > $exons_path && + tabix -s 1 -b 2 -e 3 $exons_path && +#end if +]]> + </token> + <token name="@EXONS_FILE@"> +#if 'exons_file' in $section and $section.exons_file: + --exons $exons_path +#end if + </token> + + <xml name="macro_ploidy_file"> + <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> + </xml> + <token name="@PLOIDY_FILE@"> +#if 'ploidy_file' in $section and $section.ploidy_file: + --ploidy "${section.ploidy_file}" +#end if + </token> + + <xml name="macro_collapse_opt_none"> + <option value="none">none - require the exact same set of alleles in all files</option> + </xml> + <xml name="macro_collapse_opt_id"> + <option value="id">id - only records with identical ID column are compatible. </option> + </xml> + <xml name="macro_collapse"> + <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files"> + <option value="snps">snps - allow different alleles, as long as they all are SNPs</option> + <option value="indels">indels - allow different alleles, as long as they all are indels</option> + <option value="both">both - indels and snps </option> + <option value="some">some - at least some of the ALTs must match</option> + <option value="any">any - any combination of alleles</option> + <yield/> + </param> + </xml> + <token name="@COLLAPSE@"> +#if $section.collapse: + --collapse "${section.collapse}" +#end if + </token> + + <xml name="macro_apply_filters"> + <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" + help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")"> + <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> + </param> + </xml> + <token name="@APPLY_FILTERS@"> +#if $section.apply_filters: + --apply-filters "${section.apply_filters}" +#end if + </token> + + <xml name="macro_select_output_type"> + <param name="output_type" type="select"> + <option value="b">compressed BCF</option> + <!-- no galaxy datatypes for these + <option value="u">uncompressed BCF</option> + <option value="z">compressed VCF</option> + --> + <option value="v">uncompressed VCF</option> + </param> + </xml> + <token name="@OUTPUT_TYPE@"> +#if str($output_type) != "__none__": + --output-type "${output_type}" +#end if + </token> + + <xml name="macro_vcf_output"> + <data name="output_file" format="vcf"> + <change_format> + <when input="output_type" value="b" format="bcf" /> + <when input="output_type" value="u" format="bcf" /> + <when input="output_type" value="z" format="vcf_bgzip" /> + <when input="output_type" value="v" format="vcf" /> + </change_format> + </data> + </xml> + + <xml name="macro_regions"> + <conditional name="regions"> + <param name="regions_src" type="select" label="Regions"> + <option value="__none__">None</option> + <option value="regions">regions</option> + <option value="regions_file">regions-file</option> + </param> + <when value="__none__"/> + <when value="regions"> + <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" + help="Each region is specifed as: chr or chr:pos or chr:from-to"> + <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> + </param> + </when> + <when value="regions_file"> + <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" /> + </when> + </conditional> + </xml> + <token name="@REGIONS@"> +#if $section.regions.regions_src == 'regions' and $section.regions.regions != '': + --regions "$section.regions.regions" +#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: + --regions-file "$section.regions.regions_file" +#end if + </token> + + <xml name="macro_targets_file"> + <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" > + <yield/> + </param> + <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" /> + </xml> + <token name="@PREPARE_TARGETS_FILE@"> +<![CDATA[ +#set $targets_path = None +#if 'targets' in $section + #if $section.targets.targets_src == 'targets_file': + #set $targets_path = 'targets_file.tab.gz' + bgzip -c "$section.targets.targets_file" > $targets_path && + tabix -s 1 -b 2 -e 2 $targets_path && + #end if +#elif $tgts_sec.targets_file: + #set $targets_path = 'targets_file.tab.gz' + bgzip -c "$section.targets_file" > $targets_path && + tabix -s 1 -b 2 -e 2 $targets_path && +#end if +]]> + </token> + <token name="@TARGETS_FILE@"> +<![CDATA[ +#if $targets_path is not None: + --targets-file "${section.invert_targets_file}${targets_path}" +#elif $section.targets_file: + --targets-file "${section.invert_targets_file}${section.targets_file}" +#end if +]]> + </token> + + <xml name="macro_targets"> + <conditional name="targets"> + <param name="targets_src" type="select" label="Targets"> + <option value="__none__">None</option> + <option value="targets">targets</option> + <option value="targets_file">targets-file</option> + </param> + <when value="__none__"/> + <when value="targets"> + <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" + help="Each target is specifed as: chr or chr:pos or chr:from-to"> + <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> + </param> + <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" /> + </when> + <when value="targets_file"> + <expand macro="macro_targets_file"> + <optional>true</optional> + </expand> + </when> + </conditional> + </xml> + <token name="@TARGETS@"> +<![CDATA[ +#if $targets_path: + --targets-file "${section.targets.invert_targets_file}${targets_path}" +#else: + #if $section.targets.targets_src == 'targets' and $section.targets.targets != '': + --targets "${section.targets.invert_targets_file}${section.targets.targets}" + #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: + --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" + #end if +#end if +]]> + </token> + + <xml name="macro_samples"> + <param name="samples" type="text" value="" label="Samples" optional="true" + help="(-s) comma separated list of samples to annotate (or exclude with "^" prefix)"> + <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> + </param> + <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" + help="inverts the query/filtering applied by Samples" /> + <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" + help="(-S) file of samples to include" /> + <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" + help="inverts the query/filtering applied by Samples File" /> + </xml> + <token name="@SAMPLES@"> +#set $samples_defined = False +#if str($section.samples) != '': + #set $samples_defined = True + --samples "${section.invert_samples}${section.samples}" +#end if +#if $section.samples_file: + #set $samples_defined = True + --samples-file "${section.invert_samples_file}${section.samples_file}" +#end if + </token> + + <xml name="macro_sample"> + <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" /> + </xml> + <token name="@SAMPLE@"> +#if $section.sample: + --sample "${section.sample}" +#end if + </token> + + + <xml name="macro_include"> + <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true"> + <validator type="regex" message="Single quote not allowed">^[^']*$</validator> + <sanitizer sanitize="False"/> + </param> + </xml> + <token name="@INCLUDE@"> +#if $section.include: + --include '${section.include}' +#end if + </token> + + <xml name="macro_exclude"> + <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true"> + <validator type="regex" message="Single quote not allowed">^[^']*$</validator> + <sanitizer sanitize="False"/> + </param> + </xml> + <token name="@EXCLUDE@"> +#if $section.exclude: + --exclude '${section.exclude}' +#end if + </token> + + <xml name="macro_columns"> + <param name="columns" type="text" value="" label="Columns" optional="true" + 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> + </param> + </xml> + <token name="@COLUMNS@"> +#if $section.columns != '': + --columns "${section.columns}" +#end if + </token> + + <xml name="macro_haploid2diploid"> + <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" /> + </xml> + + <xml name="macro_vcf_ids"> + <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" /> + </xml> + <token name="@VCF_IDS@"> +${section.vcf_ids} + </token> + + <token name="@OUTPUT_HELP@"> + <![CDATA[ +Output Type +----------- + +Output compressed BCF (b), or uncompressed VCF (v). +Use the BCF option when piping between bcftools subcommands to speed up +performance by removing unecessary compression/decompression +and VCF<->BCF conversion. + +This Galaxy tool recommends using the compressed BCF format +as piping is not implemented, and uncompressed data would +use unnecessary amounts of space. + +]]></token> + <token name="@REGIONS_HELP@"> + <![CDATA[ +Region Selections +----------------- + +Regions can be specified in a VCF, +BED, or tab-delimited file (the default). The columns of the +tab-delimited file are: CHROM, POS, and, optionally, POS_TO, +where positions are 1-based and inclusive. Uncompressed +files are stored in memory, while bgzip-compressed and +tabix-indexed region files are streamed. Note that sequence +names must match exactly, "chr20" is not the same as "20". +Also note that chromosome ordering in FILE will be +respected, the VCF will be processed in the order in which +chromosomes first appear in FILE. However, within +chromosomes, the VCF will always be processed in ascending +genomic coordinate order no matter what order they appear in +FILE. Note that overlapping regions in FILE can result in +duplicated out of order positions in the output. This option +requires indexed VCF/BCF files. + +]]></token> + <token name="@TARGETS_HELP@"><![CDATA[ +Targets +------- + +Similar to regions, but the next position is accessed by streaming the whole +VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be +applied simultaneously: regions uses the index to jump to a region and targets discards +positions which are not in the targets. Unlike regions, targets can be prefixed with +"^" to request logical complement. For example, "^X,Y,MT" indicates that +sequences X, Y and MT should be skipped. Yet another difference between the two +is that regions checks both start and end positions of indels, whereas targets checks +start positions only. + +For the bcftools call command, with the option -C alleles, third column of the +targets file must be comma-separated list of alleles, starting with the +reference allele. Note that the file must be compressed and index. Such a file +can be easily created from a VCF using:: + + bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz + ]]> + <!-- TODO: galaxy-ify --> + </token> + + + <token name="@COLLAPSE_HELP@"> +Collapse +-------- + +Controls how to treat records with duplicate positions and defines compatible +records across multiple input files. Here by "compatible" we mean records which +should be considered as identical by the tools. For example, when performing +line intersections, the desire may be to consider as identical all sites with +matching positions (bcftools isec -c all), or only sites with matching variant +type (bcftools isec -c snps -c indels), or only sites with all alleles +identical (bcftools isec -c none). + + ++------------+----------------------------------------------------------------+ +| Flag value | Result | ++============+================================================================+ +| none | only records with identical REF and ALT alleles are compatible | ++------------+----------------------------------------------------------------+ +| some | only records where some subset of ALT alleles match are | +| | compatible | ++------------+----------------------------------------------------------------+ +| all | all records are compatible, regardless of whether the ALT | +| | alleles match or not. In the case of records with the same | +| | position, only the first wil lbe considered and appear on | +| | output. | ++------------+----------------------------------------------------------------+ +| snps | any SNP records are compatible, regardless of whether the ALT | +| | alleles match or not. For duplicate positions, only the first | +| | SNP record will be considered and appear on output. | ++------------+----------------------------------------------------------------+ +| indels | all indel records are compatible, regardless of whether the | +| | REF and ALT alleles match or not. For duplicate positions, | +| | only the first indel record will be considered and appear on | +| | output. | ++------------+----------------------------------------------------------------+ +| both | abbreviation of "-c indels -c snps" | ++------------+----------------------------------------------------------------+ +| id | only records with identical ID column are compatible. | +| | Supportedby bcftools merge only. | ++------------+----------------------------------------------------------------+ + + </token> + + <token name="@EXPRESSIONS_HELP@"> + <![CDATA[ +Expressions +----------- + +Valid expressions may contain: + +- numerical constants, string constants + + :: + + 1, 1.0, 1e-4 + "String" + +- arithmetic operators + + :: + + +,*,-,/ + +- comparison operators + + :: + + == (same as =), >, >=, <=, <, != + +- regex operators "~" and its negation "!~" + + :: + + INFO/HAYSTACK ~ "needle" + +- parentheses + + :: + + (, ) + +- logical operators + + :: + + && (same as &), ||, | + +- INFO tags, FORMAT tags, column names + + :: + + INFO/DP or DP + FORMAT/DV, FMT/DV, or DV + FILTER, QUAL, ID, REF, ALT[0] + +- 1 (or 0) to test the presence (or absence) of a flag + + :: + + FlagA=1 && FlagB=0 + +- "." to test missing values + + :: + + DP=".", DP!=".", ALT="." + +- missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression + + :: + + GT="." + +- TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other) + + :: + + TYPE="indel" | TYPE="snp" + +- array subscripts, "*" for any field + + :: + + (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3 + DP4[*] == 0 + CSQ[*] ~ "missense_variant.*deleterious" + +- function on FORMAT tags (over samples) and INFO tags (over vector fields) + + :: + + MAX, MIN, AVG, SUM, STRLEN, ABS + +- variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes + + :: + + N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN + +**Notes:** + +- String comparisons and regular expressions are case-insensitive +- If the subscript "*" is used in regular expression search, the whole field + is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be + true for the string vector INFO/STR=AB,CD. +- Variables and function names are case-insensitive, but not tag names. For + example, "qual" can be used instead of "QUAL", "strlen()" instead of + "STRLEN()" , but not "dp" instead of "DP". + +**Examples:** + + :: + + MIN(DV)>5 + MIN(DV/DP)>0.3 + MIN(DP)>10 & MIN(DV)>3 + FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample + FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples + QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples + QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites + TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2) + MIN(DP)>35 && AVG(GQ)>50 + ID=@file .. selects lines with ID present in the file + ID!=@~/file .. skip lines with ID present in the ~/file + MAF[0]<0.05 .. select rare variants at 5% cutoff + +]]></token> + + + + +</macros>