Mercurial > repos > wrtz > bcftools
changeset 5:0e3e6581e6b1 draft
Uploaded
| author | wrtz |
|---|---|
| date | Thu, 14 Jan 2016 17:47:32 -0500 |
| parents | 2cffdec901f5 |
| children | 24fc012c3f0e |
| files | bcftools_norm.xml |
| diffstat | 1 files changed, 153 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_norm.xml Thu Jan 14 17:47:32 2016 -0500 @@ -0,0 +1,153 @@ +<tool id="bcftools_norm" name="BCFtools norm" version="1.0.0"> + <description>Left-align and normalize indels, check if REF alleles match reference, change multiallelic 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 + #if str( $fasta_ref_cond.set_fasta_ref ) == "True": + #if str( $fasta_ref_cond.fasta_ref_index ) != "None": + ln -s -f $fasta_ref_cond.fasta_ref fasta_ref_file.${fasta_ref.ext}.fa && + ln -s -f $fasta_ref_cond.fasta_ref_index fasta_ref_file.${fasta_ref.ext}.fa.fai && + #end if + #end if + /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools norm + --output "${output_file}" + --output-type "${output_type}" + #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( $check_ref_cond.set_check_ref ) == "True": + #if str( $check_ref_cond.warn ) == "true": + #if str( $check_ref_cond.check_ref ) == "None": + --check-ref "w" + #else + --check-ref "w${check_ref_cond.check_ref}" + #end if + #else + --check-ref "${check_ref_cond.check_ref}" + #end if + #end if + #if str( $fasta_ref_cond.set_fasta_ref ) == "True": + #if str( $fasta_ref_cond.fasta_ref_index ) != "None": + --fasta-ref "fasta_ref_file.${fasta_ref.ext}.fa" + #else + --fasta-ref "${fasta_ref}" + #end if + #end if + #if str( $multiallelics_cond.set_multiallelics ) == "True": + #if str( $multiallelics_cond.minus_or_plus ) == "minus": + #if str ( $multiallelics_cond.multiallelics ) != "None": + --multiallelics "-${multiallelics_cond.multiallelics}" + #else + --multiallelics "-" + #end if + #else + #if str ( $multiallelics_cond.multiallelics ) != "None": + --multiallelics "+${multiallelics_cond.multiallelics}" + #else + --multiallelics "+" + #end if + #end if + #end if + #if str( $rm_dup ) != "None": + --rm-dup "${rm_dup}" + #end if + ${do_not_normalize} + ${strict_filter} + #if str( $site_win ) != "": + --site-win "${site_win}" + #end if + #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" 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" 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> + <conditional name="fasta_ref_cond"> + <param name="set_fasta_ref" type="boolean" checked="False" label="Specify FASTA reference sequence" help="-f" /> + <when value="true"> + <param name="fasta_ref" type="data" label="FASTA reference file" help="Reference sequence. Using this option turns on left-alignment and normalization. Set corresponding index below." /> + <param name="fasta_ref_index" type="data" optional="True" label="FASTA reference index" help="Run Faidx (SAMtools) Galaxy tool on above reference file to create index. Errors can arise if this index is not specified." /> + </when> + </conditional> + <param name="do_not_normalize" type="boolean" checked="False" truevalue="--do-not-normalize" falsevalue="" label="Turn off indel normalization" help="-N. Indel normalization automatically occurs when FASTA reference is used. Use this option to disable this behavior." /> + <conditional name="check_ref_cond"> + <param name="set_check_ref" type="boolean" checked="False" label="Check REF" help="-c. Choose action when an incorrect or missing REF allele is encountered." /> + <when value="true"> + <param name="check_ref" type="select" optional="True" label="Action" help="Action when an incorrect or missing REF allele is encountered."> + <option value="e">Exit program</option> + <option value="x">Exclude incorrect/missing sites</option> + <option value="s">Set or fix incorrect/missing sites (requires FASTA reference)</option> + </param> + <param name="warn" type="boolean" checked="False" label="Warn" help="Warn when an incorrect or missing REF allele is encountered." /> + </when> + </conditional> + <param name="rm_dup" type="select" optional="True" label="Remove duplicates" help="-d. For given variant type, if a record is present in multiple files, output only the first instance."> + <option value="snps">SNPs</option> + <option value="indels">Indels</option> + <option value="both">Both (SNPs and indels)</option> + <option value="any">Any</option> + </param> + <conditional name="multiallelics_cond"> + <param name="set_multiallelics" type="boolean" checked="False" label="Modify multiallelic sites" help="-m. Split multiallelic sites into biallelic records, or join biallelic sites into multiallelic records." /> + <when value="true"> + <param name="minus_or_plus" type="select" label="Split or join"> + <option value="minus" selected="true">Split multiallelic sites into biallelic records</option> + <option value="plus">Join biallelic sites into multiallelic records</option> + </param> + <param name="multiallelics" type="select" optional="True" label="Sites to split/join" help=""> + <option value="snps">SNPs (only SNP records are split/joined)</option> + <option value="indels">Indels (only indel records are split/joined)</option> + <option value="both">Both (SNPs and indels are merged separately into two records)</option> + <option value="any">Any (SNPs and indels are merged into a single record)</option> + </param> + </when> + </conditional> + <param name="strict_filter" type="boolean" checked="False" truevalue="--strict-filter" falsevalue="" label="Strict PASS filter" help="-s. When merging biallelics into multiallelics, merged site has value PASS only if all sites being merged have value PASS." /> + <param name="site_win" type="integer" optional="true" label="Position window" help="-w. Maximum distance between two records to consider when locally sorting variants which changed position during the realignment." /> + </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 norm**: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows, recover multiallelics from multiple rows. Left-alignment and normalization will only be applied if the --fasta-ref option is supplied. + +Please see https://samtools.github.io/bcftools/bcftools.html for more info on options. + </help> +</tool> +