/tools/fastq/fastq_to_fasta.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 40 lines · 31 code · 6 blank · 3 comment · 0 complexity · 6573cdfc5a7163cdab95a4364ba5f771 MD5 · raw file

  1. <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
  2. <description>converter</description>
  3. <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
  4. <inputs>
  5. <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
  6. </inputs>
  7. <outputs>
  8. <data name="output_file" format="fasta" />
  9. </outputs>
  10. <tests>
  11. <!-- basic test -->
  12. <test>
  13. <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
  14. <output name="output_file" file="fastq_to_fasta_python_1.out" />
  15. </test>
  16. <!-- color space test -->
  17. <test>
  18. <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
  19. <output name="output_file" file="fastq_to_fasta_python_2.out" />
  20. </test>
  21. <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
  22. <test>
  23. <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
  24. <output name="output_file" file="fastq_to_fasta_python_1.out" />
  25. </test>
  26. </tests>
  27. <help>
  28. **What it does**
  29. This tool converts FASTQ sequencing reads to FASTA sequences.
  30. ------
  31. **Citation**
  32. 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;`_
  33. </help>
  34. </tool>