Mercurial > repos > jjohnson > bcftools_call
diff bcftools_call.xml @ 0:20b3aaa16d64 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 20:46:24 -0400 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_call.xml Sat Jun 25 20:46:24 2016 -0400 @@ -0,0 +1,239 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> + <description>SNP/indel variant calling from VCF/BCF</description> + <macros> + <token name="@EXECUTABLE@">call</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="aggressive"><![CDATA[ +@PREPARE_ENV@ +@PREPARE_INPUT_FILE@ +#set $section = $sec_consensus_variant_calling.variant_calling +#set $targets_path = None +#if $section.method == 'multiallelic': + #if $section.genotypes.constrain == 'alleles': + #set $section = $sec_consensus_variant_calling.variant_calling.genotypes + @PREPARE_TARGETS_FILE@ + #end if +#end if + +bcftools @EXECUTABLE@ + +#set $section = $sec_consensus_variant_calling.variant_calling +#if $section.method == 'multiallelic': + -m + #if str($section.gvcf) != '': + --gvcf $section.gvcf + #end if + #if $section.genotypes.constrain == 'alleles': + --constrain alleles $section.genotypes.insert_missed + #set $section = $sec_consensus_variant_calling.variant_calling.genotypes + @TARGETS_FILE@ + #else + #if $section.genotypes.constrain == 'trio': + --constrain trio + #if $section.genotypes.novel_rate: + --novel-rate '$section.genotypes.novel_rate' + #end if + #end if + #set $section = $sec_consensus_variant_calling.variant_calling.genotypes + @TARGETS@ + #end if +#else + -c +#end if + +#set $section = $sec_restrict +@REGIONS@ +@SAMPLES@ + +#set $section = $sec_consensus_variant_calling +#if $section.pval_threshold: + --pval-threshold "$section.pval_threshold" +#end if +#if $section.prior: + --prior "$section.prior" +#end if + +## File format section +#set $section = $sec_file_format +#if $section.ploidy: + --ploidy "${section.ploidy}" +#end if +#if $section.ploidy_file: + --ploidy-file "${section.ploidy_file}" +#end if + +## Input/output section +#set $section = $sec_input_output +${section.keep_alts} +## #if section.format_fields: +## --format-fields "${section.format_fields}" +## #end if +${section.keep_masked_ref} +#if $section.skip_variants: + --skip-variants "${section.skip_variants}" +#end if +${section.variants_only} + +@OUTPUT_TYPE@ +@THREADS@ + +## Primary Input/Outputs +@INPUT_FILE@ +> "$output_file" +]]> + </command> + <inputs> + <expand macro="macro_input" /> + <section name="sec_restrict" expanded="false" title="Restrict to"> + <expand macro="macro_regions" /> + <expand macro="macro_samples" /> + </section> + <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options"> + <conditional name="variant_calling"> + <param name="method" type="select" label="calling method"> + <option value="multiallelic">Multiallelic and rare-variant Caller</option> + <option value="consensus">Consensus Caller</option> + </param> + <when value="multiallelic"> + <conditional name="genotypes"> + <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)"> + <option value="none">Do not constrain</option> + <option value="alleles">alleles - call genotypes given alleles</option> + <option value="trio">trio - call genotypes given the father-mother-child constraint</option> + </param> + <when value="none"> + <expand macro="macro_targets" /> + </when> + <when value="alleles"> + <expand macro="macro_targets_file"/> + <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" /> + </when> + <when value="trio"> + <expand macro="macro_targets" /> + <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" /> + </when> + </conditional> + <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" /> + </when> + <when value="consensus"> + <conditional name="genotypes"> + <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)"> + <option value="none">Do not constrain</option> + <option value="trio">trio - call genotypes given the father-mother-child constraint</option> + </param> + <when value="none"> + </when> + <when value="trio"> + <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" /> + </when> + </conditional> + <expand macro="macro_targets" /> + </when> + </conditional> + <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)<FLOAT with -c" /> + <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" /> + </section> + <section name="sec_file_format" expanded="false" title="File format Options"> + <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true"> + <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option> + <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option> + <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option> + <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option> + <option value="1">1 - Treat all samples as haploid</option> + </param> + <param name="ploidy_file" type="data" format="tabular" label="Ploidy File" optional="True" help="space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> + <expand macro="macro_regions" /> + <expand macro="macro_samples" /> + </section> + <section name="sec_input_output" expanded="false" title="Input/output Options"> + <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" /> + <param name="format_fields" type="text" value="" optional="true" label="Format Fields" + help="output format fields: GQ,GP" > + <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator> + </param> + <param name="keep_masked_ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep Masked Ref" help="keep sites with masked reference allele (REF=N)" /> + <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps"> + <option value="indels">indels</option> + <option value="snps">snps</option> + </param> + <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" /> + </section> + <expand macro="macro_select_output_type" /> + </inputs> + <outputs> + <expand macro="macro_vcf_output"/> + </outputs> + <tests> + <test> + <param name="input_file" ftype="vcf" value="mpileup.vcf" /> + <param name="method" value="multiallelic" /> + <param name="variants_only" value="true" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="DP4=2,4,8,11;MQ=49" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="mpileup.vcf" /> + <param name="method" value="multiallelic" /> + <param name="gvcf" value="0" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="MinDP" /> + <has_text text="DP4=2,4,8,11;MQ=49" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="mpileup.X.vcf" /> + <param name="method" value="multiallelic" /> + <param name="ploidy_file" value="mpileup.ploidy" /> + <param name="samples_file" value="mpileup.samples" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="DP4=2,4,8,11;MQ=49" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="mpileup.X.vcf" /> + <param name="method" value="consensus" /> + <param name="output_type" value="v" /> + <param name="ploidy_file" value="mpileup.ploidy" /> + <output name="output_file"> + <assert_contents> + <has_text text="DP4=2,4,8,11" /> + <has_text text="PV4=1,1,1,1" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +================================== + bcftools @EXECUTABLE@ +================================== + +SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup. + + - This command replaces the former "bcftools view" caller. + - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. + - The original calling model can be invoked with the -c option. + +@REGIONS_HELP@ +@TARGETS_HELP@ + +@BCFTOOLS_MANPAGE@#@EXECUTABLE@ + +@BCFTOOLS_WIKI@ +]]> + </help> + <expand macro="citations" /> +</tool>