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<tool id="preprocess" name="preprocess" version="0.0.1">
  <description>
    Preprocess Tumour Normal Pairs for Cancer Genomic Workflows
  </description>
  <requirements>
    <requirement type="package" version="1.0.13">bamutil</requirement>
  </requirements>
  <command>
    <![CDATA[
    
    ln -s $input_bam input.bam;
    ln -s $input_bam.metadata.bam_index input.bam.bai;
    
    #if not $interval
      i="";
    #end if

    {
    samtools view -H input.bam;

    #if $interval
      for i in \$( cat $interval ); do
    #end if
    
    samtools view -q $filter_qual input.bam \$i
    
    #if $interval
        ; done
    #end if
    ;
    }
 
    #if $clip_overlap
        | bam clipOverlap --in -.sam --out -.sam
    #end if

    | samtools view -Sb - > $output;
    
    ]]>
  </command>
  <inputs>
    <param type="data" format="bam" name="input_bam" label="Specify BAM Alignment File"/>
    <param type="data" format="bed,txt" name="interval" label="Specify Interval" optional="true"/>
    <param type="boolean" checked="true" name="clip_overlap" label="Clip Overlaps" help="Clips overlapping region between paired reads with lowest mean quality"/>
    <param type="integer" value="0" min="0" max="255" name="filter_qual" label="Minimum Mapping Quality" help="Filter reads with quality strictly less than MMQ"/>
  </inputs>
  <outputs>
    <data format="bam" name="output"/>
  </outputs>
  <stdio>
    <exit_code range="0" level="warning" description="Normal" />
    <exit_code range="1" level="fatal" description="Error in overclipping" />
  </stdio>
</tool>