<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1">
  <description>into FASTQ</description>
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command>
  <inputs>
    <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
    <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" />
    <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>
  </inputs>
  <outputs>
    <data name="output_file" format="fastqsanger">
      <change_format>
        <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" />
        <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" />
        <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" />
        <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
      <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
      <param name="force_quality_encoding" value="None" />
      <output name="output_file" file="combine_phiX_out_1.fastqcssanger" />
    </test>
    <test>
      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
      <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
      <param name="force_quality_encoding" value="ascii" />
      <output name="output_file" file="combine_phiX_out_2.fastqcssanger" />
    </test>
    <test>
      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
      <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
      <param name="force_quality_encoding" value="None" />
      <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
    </test>
    <test>
      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
      <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
      <param name="force_quality_encoding" value="decimal" />
      <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
    </test>
    <test>
      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
      <param name="qual_file" />
      <param name="force_quality_encoding" value="decimal" />
      <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
    </test>
    <test>
      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
      <param name="qual_file" />
      <param name="force_quality_encoding" value="ascii" />
      <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" />
    </test>
  </tests>
  <help>
**What it does**

This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.

Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93).

Use this tool, for example, to convert 454-type output to FASTQ.

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