<tool id="bam_to_fastq" name="BAM to fastq" force_history_refresh="True" version="0.0.1">
  <description>Convert BAM file to fastq</description>
  <command interpreter="python">bam_to_fastq_wrapper.py $in_bam $out $out.id $__new_file_path__</command>
  <inputs>
    <param format="bam" name="in_bam" type="data" label="BAM file"/>
  </inputs>
  <outputs>
    <data format="fastqsanger" name="out" metadata_source="in_bam"/>
  </outputs>

<help>
**What it does**

Extract sequences and quality scores from a BAM file, converting into fastq files.

**Input**

A BAM alignment file. 

**Output**

Fastq files with sequence and quality data. Output qualities are in Sanger format.
For single end data, one fastq file is produced; paired end data will have separate
fastq files for the forward and reverse reads.
</help>

</tool>