<?xml version="1.0"?>

<tool id="generate_miseq_pe_bam" name="Generate a BAM file">
  <requirements>
    <requirement type="package" version="0.6.2">bwa</requirement>
  </requirements>
  
  <description>from MiSeq paired-end FASTQ files</description>
  <version_string>echo 1.0.0</version_string>
  <command interpreter="perl">bwape_parallel_optimized $__tool_data_path__ 10 ${ref_genome}.fa $read1 $read2 miseq</command>
  <inputs>
    <param format="fastqsanger" name="read1" type="data" label="FASTQ file for read number 1"/>
    <param format="fastqsanger" name="read2" type="data" label="FASTQ file for read number 2"/>
    <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the variants should be called"/>
  </inputs>
  <outputs>
    <data format="bam" label="Aligned reads against ${ref_genome}" name="outputBAM" from_work_dir="miseq.bam"/>
    <data format="text" label="Pre-dedup alignment stats" name="prededup_stats" from_work_dir="miseq.before_dedup.flagstat.txt"/>
    <data format="text" label="Alignment logfile" name="logfile" from_work_dir="miseq.align.log"/>
  </outputs>

  <tests/>

  <help>
This tool runs a pair of MiSeq FASTQ files against the human reference genome using BWA 0.6.2, deduplicates using samtools, then uses GATK to realign the reads (nearly identical to what BaseSpace alignment does).
 </help>

</tool>