Mercurial > repos > wrtz > bcftools
changeset 3:cd5b729e6cc3 draft
Uploaded
| author | wrtz |
|---|---|
| date | Thu, 14 Jan 2016 17:47:12 -0500 |
| parents | 7511152cc047 |
| children | 2cffdec901f5 |
| files | bcftools_filter.xml |
| diffstat | 1 files changed, 134 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_filter.xml Thu Jan 14 17:47:12 2016 -0500 @@ -0,0 +1,134 @@ +<tool id="bcftools_filter" name="BCFtools filter" version="1.0.0"> + <description>Apply fixed-threshold filters</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 + + /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools filter + --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( $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( $mode_plus ) == "true": + #if str( $mode_x ) == "true": + --mode +x + #else + --mode + + #end if + #elif str( $mode_x ) == "true" + --mode x + #end if + #if str( $soft_filter_cond.set_soft_filter ) == "True": + #if str( $soft_filter_cond.string_or_plus_cond.string_or_plus ) == "use_plus": + --soft-filter + + #else + --soft-filter "${soft_filter_cond.string_or_plus_cond.str}" + #end if + #end if + #if str( $set_gts_cond.set_gts ) == "True": + #if str( $set_gts_cond.gts ) == "period": + --set-GTs . + #else + --set-GTs 0 + #end if + #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"> + <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="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" label="Expression"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid> + </sanitizer> + </param> + </when> + </conditional> + <param name="mode_x" type="boolean" checked="False" label="For sites that pass filter, reset filter to "PASS"" help="-m x. Default: When FILTER string is empty, set filter to "PASS". Do not change FILTER string otherwise."/> + <param name="mode_plus" type="boolean" checked="False" label="For sites that fail filter, append new FILTER string to existing FILTER string" help="-m +. Default: Replace existing FILTER string with new FILTER string."/> + <conditional name="soft_filter_cond"> + <param name="set_soft_filter" type="boolean" checked="False" label="Annotate FILTER column" help="-s"/> + <when value="true"> + <conditional name="string_or_plus_cond"> + <param name="string_or_plus" type="select" label="Annotation string"> + <option value="use_plus" selected="true">Annotate with a pre-generated unique string ("Filter1", "Filter2", etc.)</option> + <option value="use_str">Choose annotation string</option> + </param> + <when value="use_str"> + <param name="str" type="text" label="String to annotate with" /> + </when> + </conditional> + </when> + </conditional> + <conditional name="set_gts_cond"> + <param name="set_gts" type="boolean" checked="False" label="Set genotype of samples that fail filter" help="-S"/> + <when value="true"> + <param name="gts" type="select" label="Genotype of failed samples"> + <option value="period" selected="true">.</option> + <option value="ref_allele">Reference allele</option> + </param> + </when> + </conditional> + </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 filter**: Apply fixed-threshold filters. + +Please see https://samtools.github.io/bcftools/bcftools.html for more info on options. + </help> +</tool> \ No newline at end of file