view tools/fastq/fastq_to_fasta.xml @ 1:cdcb0ce84a1b

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<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
  <description>converter</description>
  <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
  <inputs>
    <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
  </inputs>
  <outputs>
    <data name="output_file" format="fasta" />
  </outputs>
  <tests>
    <!-- basic test -->
    <test>
      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
      <output name="output_file" file="fastq_to_fasta_python_1.out" />
    </test>
    <!-- color space test -->
    <test>
      <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
      <output name="output_file" file="fastq_to_fasta_python_2.out" />
    </test>
    <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
    <test>
      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
      <output name="output_file" file="fastq_to_fasta_python_1.out" />
    </test>
  </tests>
  <help>
**What it does**

This tool converts FASTQ sequencing reads to FASTA sequences.

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**Citation**

If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_


  </help>
</tool>