<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0">
  <description>by quality score</description>
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}'
      #if $mask_type.value == 'lowercase'
      --lowercase
      #else
      -m '${mask_type}'
      #end if
  </command>
  <inputs>
    <param name="input_file" type="data" format="fastqsanger" label="File to mask" />
    <param name="mask_type" type="select" label="Mask input with">
      <option value="N">N's</option>
      <option value="lowercase">Lowercase</option>
    </param>
    <param name="score_comparison" type="select" label="When score is">
      <option value="le" selected="True">Less than or equal</option>
      <option value="lt">Less than</option>
      <option value="eq">Equal to</option>
      <option value="ne">Not Equal to</option>
      <option value="ge">Greater than</option>
      <option value="gt">Greater than or equal</option>
    </param>
    <param name="quality_score" type="integer" value="0" label="Quality score"/>
  </inputs>
  <outputs>
    <data name="output_file" format="fastqsanger" />
  </outputs>
  <tests>
    <test>
      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
      <param name="mask_type" value="N" />
      <param name="score_comparison" value="le" />
      <param name="quality_score" value="20" />
      <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" />
    </test>
    <test>
      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
      <param name="mask_type" value="lowercase" />
      <param name="score_comparison" value="le" />
      <param name="quality_score" value="20" />
      <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" />
    </test>
  </tests>
  <help>
**What it does**

This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.

This tool is not available for use on color space (csSanger) formats.

  </help>
  
  <citations>
    <citation type="doi">10.1093/bioinformatics/btq281</citation>
  </citations>
  
</tool>