Mercurial > repos > lomereiter > sambamba_filter
view sambamba_filter.xml @ 0:668e187566d5
uploaded xml wrapper
author | lomereiter |
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date | Mon, 13 Aug 2012 02:13:09 -0400 |
parents | |
children | 806b3253c996 |
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<tool id="sambamba_filter" name="Filter BAM or SAM" version="0.2.3"> <requirements> <requirement type="binary">sambamba</requirement> </requirements> <description> on flags, fields, and tags </description> <command> #if $query != None: #set $query = $query.replace('__sq__', '\'') #set $query = $query.replace('__ob__', '[') #set $query = $query.replace('__cb__', ']') #set $query = $query.replace('__dq__', '"') #set $query = $query.replace('__oc__', '{') #set $query = $query.replace('__cc__', '}') #set $query = $query.replace('__gt__', chr(62)) #set $query = $query.replace('__lt__', chr(60)) #end if #if $outputformat.format == 'bam': #set $header = '' #else #set $header = $outputformat.header #end if #if isinstance($input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__): #set $input1 = 'input.bam' ln -s $input $input1 && ln -s $input.metadata.bam_index input.bai && sambamba view --filter="$query" -f $outputformat.format -o $outfile $input1 $header $region #else sambamba view -S --filter="$query" -f $outputformat.format -o $outfile $input $header #end if </command> <inputs> <param name="input" type="data" format="bam,sam" label="BAM or SAM file to filter"/> <param name="query" type="text" size="80"> <label>Filter expression</label> <help> The syntax is described at sambamba wiki: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax </help> </param> <conditional name="outputformat"> <param name="format" type="select"> <label>Output format</label> <option value="sam">SAM</option> <option value="bam">BAM</option> </param> <when value="sam"> <param name="header" type="select"> <label>Include SAM header in output</label> <option value="-h">Yes</option> <option value="">No</option> </param> </when> <when value="bam"/> </conditional> <param name="region" type="text" size="40" label="Region in format chr:beg-end, works for BAM input only"> <help> The syntax is the same as in samtools, start and end coordinates are 1-based. </help> </param> </inputs> <outputs> <data name="outfile" format="bam"> <change_format> <when input="outputformat.format" value="sam" format="sam"/> </change_format> </data> </outputs> <help> **What it does** This tool uses sambamba view to filter BAM/SAM on flags, fields, tags, and region. In order to install sambamba, visit its website_ and either download a Debian package for your architecture, or build the tool from source. Input is SAM or BAM file, output is chosen by user. **Note** Filtering by region works only for coordinate-sorted BAM files. For SAM files this parameter is just ignored. ----- .. _website: http://github.com/lomereiter/sambamba </help> <!-- TODO: tests --> </tool>