<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools bamtofastq
        $tags
        -i '$input'
        -fq '$output'
        #if $fq2:
           -fq2 '$output2'
        #end if
    </command>
    <inputs>
        <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end.
            Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
    </inputs>
    <outputs>
        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
        <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
            <filter>fq2 is True</filter>
        </data>
    </outputs>
<help>

**What it does**

bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.

@REFERENCES@

    </help>
    <expand macro="citations" />
</tool>