Mercurial > repos > wrtz > bcftools
changeset 16:bb21cedd0dc9 draft
Uploaded
| author | wrtz |
|---|---|
| date | Thu, 14 Jan 2016 17:51:20 -0500 |
| parents | 9d96f73b875f |
| children | c34371f08c6f |
| files | bcftools_view.xml |
| diffstat | 1 files changed, 224 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_view.xml Thu Jan 14 17:51:20 2016 -0500 @@ -0,0 +1,224 @@ +<tool id="bcftools_view" name="BCFtools view" version="1.0.0"> + <description>Convert, view, subset, and filter VCF/BCF files</description> + <command> + #if str( $input_file_index ) != "None": + ln -s -f $input input_file.${input.ext} && + ln -s -f $input_file_index input_file.${input.ext}.tbi && + #end if + bcftools view + ${drop_genotypes} + ${header_only} + ${no_header} + --output-file "${output_file}" + --output-type "${output_type}" + #if str( $regions ) != "": + --regions "${regions}" + #end if + #if str( $targets ) != "": + --targets "${targets}" + #end if + #if str( $samples ) != "": + --samples "${samples}" + #end if + #if str( $regions_file ) != "None": + --regions-file "${regions_file}" + #end if + #if str( $targets_file ) != "None": + --targets-file "${targets_file}" + #end if + #if str( $samples_file ) != "None": + --samples-file "${samples_file}" + #end if + #if str( $apply_filters ) != "": + --apply-filters "${apply_filters}" + #end if + #if str( $min_ac_cond.set_min_ac ) == "True": + --min-ac $min_ac_cond.min_ac:$min_ac_cond.min_ac_type + #end if + #if str( $max_ac_cond.set_max_ac ) == "True": + --max-ac $max_ac_cond.max_ac:$max_ac_cond.max_ac_type + #end if + #if str( $min_af_cond.set_min_af ) == "True": + --min-af $min_af_cond.min_af:$min_af_cond.min_af_type + #end if + #if str( $max_af_cond.set_max_af ) == "True": + --max-af $max_af_cond.max_af:$max_af_cond.max_af_type + #end if + #if str( $expr_cond.set_expr ) == "True": + #if str( $expr_cond.include_or_exclude ) == "include": + --include "${expr_cond.expr}" + #else + --exclude "${expr_cond.expr}" + #end if + #end if + #if str( $genotype_cond.set_genotype ) == "True": + #if str( $genotype_cond.include_or_exclude ) == "include": + --genotype $genotype_cond.genotype + #else + --genotype ^$genotype_cond.genotype + #end if + #end if + #if str( $var_type_cond.set_var_type ) == "True": + #if str( $var_type_cond.include_or_exclude ) == "include": + --types $var_type_cond.var_types + #else + --exclude-types $var_type_cond.var_types + #end if + #end if + ${uncalled} + ${exclude_uncalled} + ${private} + ${exclude_private} + + #if str( $input_file_index ) != "None": + input_file.${input.ext} + #else + $input + #end if + </command> + + <inputs> + <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/> + <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/> + <param name="output_type" type="select" label="Output data type" help="-O"> + <option value="v" selected="true">VCF</option> + <option value="b">BCF</option> + </param> + <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/> + <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]"> + <sanitizer invalid_char=""> + <valid initial="string.digits"><add value="CHRchr-:,"/> </valid> + </sanitizer> + </param> + <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/> + <param name="targets" type="text" size="80" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]"> + <sanitizer invalid_char=""> + <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid> + </sanitizer> + </param> + <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/> + <param name="samples" type="text" size="80" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" /> + <param name="apply_filters" type="text" size="80" optional="True" label="Apply filters" help="-f. Comma-separated list of strings. Keeps only sites where FILTER column contains one of these strings." /> + <param name="drop_genotypes" type="boolean" checked="False" truevalue="--drop-genotypes" falsevalue="" label="Drop individual genotype information" help="-G" /> + <param name="no_header" type="boolean" checked="False" truevalue="--no-header" falsevalue="" label="Suppress the header in VCF output" help="-H" /> + <param name="header_only" type="boolean" checked="False" truevalue="--header-only" falsevalue="" label="Output the VCF header only" help="-h" /> + <conditional name="min_ac_cond"> + <param name="set_min_ac" type="boolean" checked="False" label="Set minimum allele count" help="-c" /> + <when value="true"> + <param name="min_ac" type="integer" optional="true" label="Minimum allele count" help="Minimum allele count of sites to be printed, for given allele type." /> + <param name="min_ac_type" type="select" label="Allele type"> + <option value="nref" selected="True">Non-reference</option> + <option value="alt1">1st alternate</option> + <option value="minor">Minor (least frequent)</option> + <option value="major">Major (most frequent)</option> + <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option> + </param> + </when> + </conditional> + <conditional name="max_ac_cond"> + <param name="set_max_ac" type="boolean" checked="False" label="Set maximum allele count" help="-C" /> + <when value="true"> + <param name="max_ac" type="integer" optional="true" label="Maximum allele count" help="Maximum allele count of sites to be printed, for given allele type." /> + <param name="max_ac_type" type="select" label="Allele type"> + <option value="nref" selected="True">Non-reference</option> + <option value="alt1">1st alternate</option> + <option value="minor">Minor (least frequent)</option> + <option value="major">Major (most frequent)</option> + <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option> + </param> + </when> + </conditional> + + <conditional name="min_af_cond"> + <param name="set_min_af" type="boolean" checked="False" label="Set minimum allele frequency" help="-q" /> + <when value="true"> + <param name="min_af" type="integer" optional="true" label="Minimum allele frequency" help="Minimum allele frequency of sites to be printed, for given allele type." /> + <param name="min_af_type" type="select" label="Allele type"> + <option value="nref" selected="True">Non-reference</option> + <option value="alt1">1st alternate</option> + <option value="minor">Minor (least frequent)</option> + <option value="major">Major (most frequent)</option> + <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option> + </param> + </when> + </conditional> + <conditional name="max_af_cond"> + <param name="set_max_af" type="boolean" checked="False" label="Set maximum allele frequency" help="-Q" /> + <when value="true"> + <param name="max_af" type="integer" optional="true" label="Maximum allele frequency" help="Maximum allele frequency of sites to be printed, for given allele type." /> + <param name="max_af_type" type="select" label="Allele type"> + <option value="nref" selected="True">Non-reference</option> + <option value="alt1">1st alternate</option> + <option value="minor">Minor (least frequent)</option> + <option value="major">Major (most frequent)</option> + <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option> + </param> + </when> + </conditional> + + <conditional name="genotype_cond"> + <param name="set_genotype" type="boolean" checked="False" label="Filter by genotype" help="-g. Include only, or exclude, sites with one or more of given genotype."/> + <when value="true"> + <param name="include_or_exclude" type="select" label="Include or exclude by genotype"> + <option value="include">Include</option> + <option value="exclude">Exclude</option> + </param> + <param name="genotype" type="select" label="Genotype"> + <option value="hom">Homozygous</option> + <option value="het">Heterozygous</option> + <option value="miss">Missing</option> + </param> + </when> + </conditional> + + <conditional name="expr_cond"> + <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, -e. Include/ exclude sites for which expression is true. Must use valid expression."/> + <when value="true"> + <param name="include_or_exclude" type="select" label="Include or exclude by expression"> + <option value="include">Include</option> + <option value="exclude">Exclude</option> + </param> + <param name="expr" type="text" size="80" label="Expression"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid> + </sanitizer> + </param> + </when> + </conditional> + + <conditional name="var_type_cond"> + <param name="set_var_type" type="boolean" checked="False" label="Filter by variant type" help="-v, -V. Include/ exclude sites where any ALT allele is one of the given variant types."/> + <when value="true"> + <param name="include_or_exclude" type="select" label="Include or exclude by variant type"> + <option value="include">Include</option> + <option value="exclude">Exclude</option> + </param> + <param name="var_types" type="select" multiple="true" display="checkboxes" label="Variant type"> + <option value="snps">SNPs</option> + <option value="indels">Indels</option> + <option value="mnps">MNPs</option> + <option value="other">Other</option> + </param> + </when> + </conditional> + + <param name="uncalled" type="boolean" checked="False" truevalue="--uncalled" falsevalue="" label="Print sites without a called genotype" help="-u" /> + <param name="exclude_uncalled" type="boolean" checked="False" truevalue="--exclude-uncalled" falsevalue="" label="Exclude sites without a called genotype" help="-U" /> + <param name="private" type="boolean" checked="False" truevalue="--private" falsevalue="" label="Print sites where only the subset samples carry a non-reference allele" help="-x. Requires samples file or samples list."/> + <param name="exclude_private" type="boolean" checked="False" truevalue="--exclude-private" falsevalue="" label="Exclude sites where only the subset samples carry a non-reference allele" help="-X. Requires samples file or samples list."/> + </inputs> + <outputs> + <data name="output_file" format="vcf" label="${tool.name} on ${on_string}"> + <change_format> + <when input="output_type" value="b" format="bcf" /> + </change_format> + </data> + </outputs> + <help> +**About this tool** + +**BCFtools view**: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF. Former bcftools subset. + +Please see https://samtools.github.io/bcftools/bcftools.html for more info on options. + </help> +</tool>