Mercurial > repos > wrtz > bcftools
changeset 14:818ab4af6410 draft
Uploaded
| author | wrtz |
|---|---|
| date | Thu, 14 Jan 2016 17:51:03 -0500 |
| parents | 22d009d35145 |
| children | 9d96f73b875f |
| files | bcftools_query.xml |
| diffstat | 1 files changed, 107 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_query.xml Thu Jan 14 17:51:03 2016 -0500 @@ -0,0 +1,107 @@ +<tool id="bcftools_query" name="BCFtools query" version="1.0.0"> + <description>Output VCF/BCF fields in user-defined format</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 query + --output "${output_file}" + --format "${format}" + #if str( $regions_file ) != "None": + --regions-file "${regions_file}" + #end if + #if str( $regions ) != "": + --regions "${regions}" + #end if + #if str( $targets_file ) != "None": + --targets-file "${targets_file}" + #end if + #if str( $targets ) != "": + --targets "${targets}" + #end if + #if str( $samples_file ) != "None": + --samples-file "${samples_file}" + #end if + #if str( $samples ) != "": + --samples "${samples}" + #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( $collapse ) != "None": + --collapse "${collapse}" + #end if + ${print_header} + ${list_samples} + ${allow_undef_tags} + + #if str( $input_file_index ) != "None": + input_file.${input.ext} + #else + $input + #end if + </command> + <inputs> + <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/> + <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/> + <param name="format" type="text" size="80" label="Output format string (required)" help="-f. Example: "%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n". See BCFtools documentation for more info."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid> + </sanitizer> + </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 ^)" /> + <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="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid> + </sanitizer> + </param> + </when> + </conditional> + <param name="collapse" optional="True" type="select" label="Collapse records" help="-c. Controls how to treat records with duplicate positions, and defines compatible records across multiple input files."> + <option value="some">Some (only records where some subset of ALT alleles match are compatible)</option> + <option value="all">All (all records are compatible, regardless of whether ALT alleles match)</option> + <option value="snps">SNPs (all SNP records are compatible, regardless of whether ALT alleles match) </option> + <option value="indels">Indels (all indel records are compatible, regardless of whether REF and ALT alleles match) </option> + <option value="both">Both (SNPs are compatible and indels are compatible)</option> + </param> + <param name="print_header" type="boolean" checked="False" truevalue="--print-header" falsevalue="" label="Print header" help="-H" /> + <param name="list_samples" type="boolean" checked="False" truevalue="--list-samples" falsevalue="" label="Print sample names to stdout, then exit" help="-l" /> + <param name="allow_undef_tags" type="boolean" checked="False" truevalue="--allow-undef-tags" falsevalue="" label="Allow undefined tags" help="-u. If there are undefined tags in the format string, print "." instead of throwing an error." /> + </inputs> + <outputs> + <data name="output_file" format="txt" label="${tool.name} on ${on_string}" /> + </outputs> + <help> +**About this tool** + +**BCFtools query**: Extract fields from VCF or BCF files and output them in user-defined format. + +Please see https://samtools.github.io/bcftools/bcftools.html for more info on options. + </help> +</tool>