/tools/fastx_toolkit/fastx_reverse_complement.xml

https://bitbucket.org/ialbert/galaxy-genetrack · XML · 52 lines · 37 code · 13 blank · 2 comment · 0 complexity · 31247ca3a8c29e30a3d6656d27cd47ff MD5 · raw file

  1. <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
  2. <description>sequences</description>
  3. <command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command>
  4. <inputs>
  5. <param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
  6. </inputs>
  7. <tests>
  8. <test>
  9. <!-- Reverse-complement a FASTA file -->
  10. <param name="input" value="fastx_rev_comp1.fasta" />
  11. <output name="output" file="fastx_reverse_complement1.out" />
  12. </test>
  13. <test>
  14. <!-- Reverse-complement a FASTQ file -->
  15. <param name="input" value="fastx_rev_comp2.fastq" />
  16. <output name="output" file="fastx_reverse_complement2.out" />
  17. </test>
  18. </tests>
  19. <outputs>
  20. <data format="input" name="output" metadata_source="input" />
  21. </outputs>
  22. <help>
  23. **What it does**
  24. This tool reverse-complements each sequence in a library.
  25. If the library is a FASTQ, the quality-scores are also reversed.
  26. --------
  27. **Example**
  28. Input FASTQ file::
  29. @CSHL_1_FC42AGWWWXX:8:1:3:740
  30. TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
  31. +CSHL_1_FC42AGWWWXX:8:1:3:740
  32. 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
  33. Output FASTQ file::
  34. @CSHL_1_FC42AGWWWXX:8:1:3:740
  35. TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
  36. +CSHL_1_FC42AGWWWXX:8:1:3:740
  37. 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
  38. </help>
  39. </tool>