Mercurial > repos > wrtz > bcftools
changeset 1:c511cd4b54e5 draft
Uploaded
| author | wrtz |
|---|---|
| date | Thu, 14 Jan 2016 17:46:57 -0500 |
| parents | 4f0ad5b55c62 |
| children | 7511152cc047 |
| files | bcftools_annotate.xml |
| diffstat | 1 files changed, 132 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_annotate.xml Thu Jan 14 17:46:57 2016 -0500 @@ -0,0 +1,132 @@ +<tool id="bcftools_annotate" name="BCFtools annotate" version="1.0.0"> + <description>Add or remove annotations</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( $annotations_cond.set_annotations ) == "True": + ln -s -f $annotations_cond.annotations annot_file.${annotations_cond.annotations.ext} && + ln -s -f $annotations_cond.annotations_index annot_file.${annotations_cond.annotations.ext}.tbi && + #end if + /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools annotate + --output "${output_file}" + --output-type "${output_type}" + #if str( $regions_file ) != "None": + --regions-file "${regions_file}" + #end if + #if str( $annotations_cond.set_annotations ) == "True": + --annotations annot_file.${annotations_cond.annotations.ext} + #if str( $annotations_cond.columns ) != "": + --columns "${annotations_cond.columns}" + #end if + #if str( $annotations_cond.mark_sites_cond.set_mark_sites ) == "True": + --mark-sites + #if str( $annotations_cond.mark_sites_cond.present_or_absent ) == "present": + "+${annotations_cond.mark_sites_cond.new_tag}" + #else + "-${annotations_cond.mark_sites_cond.new_tag}" + #end if + #end if + #end if + #if str( $regions ) != "": + --regions "${regions}" + #end if + #if str( $samples_file ) != "None": + --samples-file "${samples_file}" + #end if + #if str( $samples ) != "": + --samples "${samples}" + #end if + #if str( $header_lines ) != "None": + --header-lines "${header_lines}" + #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( $rename_chrs ) != "None": + --rename-chrs "${rename_chrs}" + #end if + #if str( $remove ) != "": + --remove "${remove}" + #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> + <conditional name="annotations_cond"> + <param name="set_annotations" type="boolean" checked="False" label="Set annotation file" help="-a, -c, -m"/> + <when value="true"> + <param name="annotations" type="data" label="Compressed annotation file" help="-a. Bgzip-compressed VCF/ BED/ tab-delimited file with annotations. Run Bgzip Galaxy tool to compress annotation file."/> + <param name="annotations_index" type="data" label="Compressed annotation file index" help="Tabix-generated index for annotation file. Run Tabix Galaxy tool on bgzipped annotation file to create index."/> + <param name="columns" type="text" label="Annotation file columns" help="-c. Comma-separated list of columns or tags to carry over from the annotation file." /> + + <conditional name="mark_sites_cond"> + <param name="set_mark_sites" type="boolean" checked="False" label="Mark present/absent sites" help="-m. Annotate sites which are present or absent in the annotation file with a new INFO/TAG flag. Note: BCFtools has not implemented this yet for VCF files."/> + <when value="true"> + <param name="present_or_absent" type="select" label="Mark present or absent sites"> + <option value="present">Present</option> + <option value="absent">Absent</option> + </param> + <param name="new_tag" type="text" label="New INFO/TAG flag" /> + </when> + </conditional> + + </when> + </conditional> + + <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="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" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" /> + <param name="header_lines" type="data" optional="true" label="Header lines" help="-h. File containing lines to append to VCF header."/> + <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="rename_chrs" type="data" optional="true" label="Rename chromosomes" help="--rename-chrs. File containing chromosome renaming map, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line."/> + <param name="remove" type="text" label="List of annotations to remove" help="-x. Comma-separated list of annotations to remove." /> + </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 annotate**: Add or remove annotations. + +Please see https://samtools.github.io/bcftools/bcftools.html for more info on options. + </help> +</tool> \ No newline at end of file