<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>
    <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
        #set $input1 = 'input.bam'
        ln -s $input $input1 &amp;&amp;
        ln -s $input.metadata.bam_index input.bai &amp;&amp;
        sambamba view -t \${GALAXY_SLOTS:-8}
        #if $query != "":
            --filter="$query"
        #end if
         -f bam -o $outfile $input1 $region
    </command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM or SAM file to filter"/>
        <param name="query" type="text" size="80">
            <label>Filter expression</label>
            <help>See below for query syntax.</help>
        </param>
     
        <param name="region" type="text" size="40" label="Region in format chr:beg-end">
        <help>
            Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' (region between 1,000,000 and 2,000,000bp including the end points). The coordinates are 1-based.
        </help>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format="bam"></data>
    </outputs>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occured" />
    </stdio>
    <tests>
        <test>
            <param name="input" value="ex1_header.sam" ftype="sam" />
            <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
            <param name="format" value="bam" />
            <param name="region" value="" />
            <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" />
        </test>
        <test>
            <param name="input" value="c1215_fixmate.bam" ftype="bam" />
            <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />
            <param name="format" value="sam" />
            <param name="region" value="AL096846:1000-5000" />
            <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" />     
        </test>
    </tests>
    <help>
Sambamba Filter Overview
========================

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.

You can use ``==,`` ``!=,`` ``&gt;``, ``&lt;``, ``&gt;=``, ``&lt;=`` comparison operators for both integers and strings.

Strings are delimited by single quotes, if you need a single quote inside a string, escape it with ``\\``.

Examples of filter expressions
------------------------------

::

    mapping_quality >= 30 and ([RG] =~ /^abcd/ or [NM] == 7)
    read_name == 'abc\'def'

Basic conditions for flags
--------------------------

The following flag names are recognized:
  * paired
  * proper_pair
  * unmapped
  * mate_is_unmapped
  * reverse_strand
  * mate_is_reverse_strand
  * first_of_pair
  * second_of_pair
  * secondary_alignment
  * failed_quality_control
  * duplicate

Example
~~~~~~~

::

    not (unmapped or mate_is_unmapped) and first_of_pair

Basic conditions for fields
---------------------------

Conditions for integer and string fields are supported.

List of integer fields:
  * ref_id
  * position
  * mapping_quality
  * sequence_length
  * mate_ref_id
  * mate_position
  * template_length


List of string fields:
  * read_name
  * sequence
  * cigar


Example
~~~~~~~

::

    ref_id == 3 and mapping_quality >= 50 and sequence_length >= 80

Basic conditions for tags
-------------------------

Tags are denoted by their names in square brackets, for instance, ``[RG]`` or ``[Q2].`` They support conditions for both integers and strings, i.e. the tag must also hold value of the corresponding type.

In order to do filtering based on the presence of a particular tag, you can use special ``null`` value.

Example
~~~~~~~

::

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

-----

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

    </help>
</tool>