comparison sambamba_filter.xml @ 5:123168c85390

updated to 0.4.7; use precompiled binaries

4:6d875183e6f7

<tool id="sambamba_filter" name="Filter BAM or SAM" version="1.0">
    <requirements>
        <requirement type="package" version="0.3.3">sambamba</requirement>
    </requirements>
    <description>
        on flags, fields, and tags using Sambamba
    </description>
    <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command>

            #set $query = $query.replace('__lt__', chr(60))
        #end if
        #set $input1 = 'input.bam'
        ln -s $input $input1 &&
        ln -s $input.metadata.bam_index input.bai &&
        sambamba view 
        #if $query != "":
            --filter="$query"
        #end if
         -f bam -o $outfile $input1 $region
    </command>

This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.


Filter Syntax 
=============

Complete documentation of filter syntax is available at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax.

A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.

*Basic condition* is a one for a single record field, tag, or flag.

    [RG] != null and [AM] == 37

-----

.. _sambamba: http://github.com/lomereiter/sambamba
.. _filter-syntax: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax

    </help>
</tool>

5:123168c85390

<tool id="sambamba_filter" name="Filter BAM or SAM" version="1.1">
    <requirements>
        <requirement type="package" version="0.4.7">sambamba</requirement>
    </requirements>
    <description>
        on flags, fields, and tags using Sambamba
    </description>
    <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command>

            #set $query = $query.replace('__lt__', chr(60))
        #end if
        #set $input1 = 'input.bam'
        ln -s $input $input1 &&
        ln -s $input.metadata.bam_index input.bai &&
        sambamba view -t \${GALAXY_SLOTS:-8}
        #if $query != "":
            --filter="$query"
        #end if
         -f bam -o $outfile $input1 $region
    </command>

This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.


Filter Syntax 
=============

A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.

*Basic condition* is a one for a single record field, tag, or flag.

    [RG] != null and [AM] == 37

-----

.. _sambamba: http://github.com/lomereiter/sambamba

    </help>
</tool>