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<tool id="seal_demux" name="Demux" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4" force_history_refresh="True">
  <description>Demultiplex Illumina runs on Hadoop</description>
  <requirements>
    <requirement type="package" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">seal</requirement>
    <requirement type="package" version="0.11">pydoop</requirement>
    <requirement type="package" version="0.1.3">hadoop-galaxy</requirement>
  </requirements>

  <command interpreter="python">
    demux_galaxy.py
    $input_data
    $mismatches
    $__new_file_path__
    #if $num_reducers
      $num_reducers
    #else
      null
    #end if
    $output1
    $output1.id
    $sample_sheet
    $input_format
    $output_format
    $output_compression
    #if $index.specify_index == 'present'
      true
    #else if $index.specify_index == 'not_present'
      false
    #else if $index.specify_index == 'dynamic'
      $index_present
    #else
      #raise ValueError('Invalid index value!')
    #end if
    $separate_reads
  </command>

  <inputs>
    <param name="input_data" type="data" format="pathset" label="Source data set"/>
    <param name="sample_sheet" type="data" format="csv" label="Sample sheet" />

    <conditional name="index">
      <param name="specify_index" type="select" label="Index read" default="present">
        <option value="present">Present</option>
        <option value="not_present">Not present</option>
        <option value="dynamic">Determine at runtime</option>
      </param>
      <when value="dynamic">
        <param name="index_present" type="data" />
      </when>
    </conditional>

    <param name="mismatches"
      label="Barcode base mismatch limit"
      type="integer"
      value="0"
      min="0"
      max="3" />
    <param name="num_reducers"
      label="Number of reduce tasks"
      type="integer"
      value="90"
      min="1"
      optional="true"
      />
    <param name="input_format" type="select" label="Input data format" default="qseq">
      <option value="qseq">Qseq</option>
      <option value="fastq">Fastq</option>
    </param>
    <param name="output_format" type="select" label="Output data format" default="qseq">
      <option value="qseq">Qseq</option>
      <option value="fastq">Fastq</option>
    </param>
    <param name="output_compression" type="select" label="Output compression" default="none">
      <option value="none">None</option>
      <option value="gzip">Gzip</option>
      <option value="bzip2">Bzip2</option>
    </param>

    <param name="separate_reads" type="boolean"
      label="Separate reads by read number"
      default="false"
      truevalue="separate-reads"
      />
  </inputs>

  <outputs>
    <data name="output1" format="pathset" label="Demuxed" />
  </outputs>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>

  <help>
    Demux is a Hadoop utility to demultiplex data from multiplexed Illumina runs.
  </help>
</tool>