<tool id="sambamba_filter" name="Filter BAM or SAM" version="0.2.4">
    <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 = $query.replace('__lt__', chr(60))
        #end if
        #if isinstance($input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__):
            #set $input1 = 'input.bam'
            ln -s $input $input1 &amp;&amp;
            ln -s $input.metadata.bam_index input.bai &amp;&amp;
            sambamba view -h --filter="$query" -f $outputformat.format -o $outfile $input1 $region
        #else
            sambamba view -S -h --filter="$query" -f $outputformat.format -o $outfile $input
        #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">
            <!-- TODO
                <param name="header" type="select">
                    <label>Include SAM header in output</label>
                    <option value="yes">Yes</option>
                    <option value="no">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>
    <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="header" value="yes" />-->
            <param name="region" value="AL096846:1000-5000" />
            <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" />     
        </test>
    </tests>
    <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 ignored.

-----

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


    </help>
</tool>