<tool id="fastq_groomer_parallel" name="FASTQ Parallel Groomer" version="0.3.0">
  <description>Parallel Implementation of FASTQ Groomer</description>
  <command interpreter="python">fastq_groomer_parallel.py '$input_file' '$input_type' '$output_file'
#if str( $options_type['options_type_selector'] ) == 'basic':
#if str( $input_type ) == 'cssanger':
'cssanger'
#else:
'sanger'
#end if
'ascii' 'summarize_input'
#else:
'${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}'
#end if
'2'
</command>
  <inputs>
    <param name="input_file" type="data" format="fastq" label="File to groom" />
    <param name="input_type" type="select" label="Input FASTQ quality scores type">
      <option value="solexa">Solexa</option>
      <option value="illumina">Illumina 1.3-1.7</option>
      <option value="sanger" selected="True">Sanger</option>
      <option value="cssanger">Color Space Sanger</option>
    </param>
    <conditional name="options_type">
    <param name="options_type_selector" type="select" label="Advanced Options">
      <option value="basic" selected="True">Hide Advanced Options</option>
      <option value="advanced">Show Advanced Options</option>
    </param>
    <when value="basic">
      <!-- no options -->
    </when>
    <when value="advanced">
      <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format.">
        <option value="solexa">Solexa</option>
        <option value="illumina">Illumina 1.3+</option>
        <option value="sanger" selected="True">Sanger (recommended)</option>
        <option value="cssanger">Color Space Sanger</option>
      </param>
      <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
        <option value="None">Use Source Encoding</option>
        <option value="ascii" selected="True">ASCII</option>
        <option value="decimal">Decimal</option>
      </param>
      <param name="summarize_input" type="select" label="Summarize input data">
        <option value="summarize_input" selected="True">Summarize Input</option>
        <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
      </param>
    </when>
  </conditional>
  </inputs>
  <outputs>
    <data name="output_file" format="fastqsanger">
      <change_format>
        <when input="input_type" value="cssanger" format="fastqcssanger" />
        <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
        <when input="options_type.output_type" value="illumina" format="fastqillumina" />
        <when input="options_type.output_type" value="sanger" format="fastqsanger" />
        <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
    <!-- Unfortunately, cannot test for expected failures -->
  </tests>
  <help>
**What it does**

This is a parallel implementation of FASTQ Groomer. It utilizes multiple CPUs thus runs much faster than the original implementation.
  </help>
</tool>