<tool id="sam_to_fastq" name="SAM to FASTQ" version="0.1">
  <description></description>
  <command interpreter="python">sam_to_fastq.py --input $input --output $output</command>
  <inputs>
       <param name="input" type="data" format="sam" label="SAM file for extraction of aligned reads in FASTQ format"/>
   </inputs>

 <outputs>
   <data format="fastqsanger" name="output" label="FASTQ extraction" />
</outputs>

    <tests>
        <test>
            <param ftype="fasta" name="input" value="input.sam" />
            <output file="output.fastq" name="output" />
        </test>
    </tests>


<help>

**What it does**

Extract sequence and sequence quality of aligned reads in a SAM alignment file and return a FASTQ file containing those reads

</help>

</tool>