<tool id="pairScan" name="Scan paired-end reads for overlap" version="1.0.0.3">
  <description> Scan paired-end reads for overlap </description>
  <requirements>
    <requirement type="package">python-levenshtein</requirement>
  </requirements>
  <required_files>
    <include type="literal" path="pairScan.py"/>
  </required_files>

  <command>
    python '$__tool_directory__'/pairScan.py -f $fasta_input -o $min_overlap -m $max_mismatch -p $pass -b $bad -s $offset
  </command>

  <inputs>
    <param format="fasta" type="data" name="fasta_input" label="Reads in FASTA format" />
    <param name="min_overlap" type="integer" size="3" value="30" min="20" max="100" label="Minimum overlap length [nt] " />
    <param name="max_mismatch" type="select" label="Maximum number of mismatches per 100 bp">
      <option value="0">0</option>
      <option value="1" selected="true">1</option>
      <option value="2">2</option>
      <option value="3">3</option>
      <option value="4">4</option>
    </param>
    <param name="offset" type="select" label="Maximum offset">
      <option value="0">0</option>
      <option value="1">1</option>
      <option value="2">2</option>
      <option value="3">3</option>
      <option value="4">4</option>
      <option value="5" selected="true" >5</option>
      <option value="6">6</option>
      <option value="7">7</option>
      <option value="8">8</option>
      <option value="9">9</option>
      <option value="10">10</option>
    </param>
    
    
    
  </inputs>


  <outputs>
    <data format="fasta" name="pass" label="Pairs with no overlap from dataset ${fasta_input.hid}"/>
   	<data format="fasta" name="bad" label="Overlaping pairs from dataset ${fasta_input.hid}"/>
  </outputs>

  <help>
    **Scan paired reads for overlap**
    
  </help>

  
</tool>