/tools/metag_tools/fastqsolexa_to_fasta_qual.xml

https://bitbucket.org/ialbert/galaxy-genetrack · XML · 91 lines · 69 code · 21 blank · 1 comment · 0 complexity · c74a453bc2e777e0b69e8231800e5db4 MD5 · raw file

  1. <tool id="fastqsolexa_to_fasta_qual" name="FASTQSOLEXA-to-FASTA-QUAL" version="1.0.0">
  2. <description>extracts sequences and quality scores from FASTQSOLEXA data</description>
  3. <command interpreter="python">fastqsolexa_to_fasta_qual.py $input1 $output1 $output2 $input1.extension</command>
  4. <inputs>
  5. <param name="input1" type="data" format="fastqsolexa" label="Fastqsolexa file"/>
  6. </inputs>
  7. <outputs>
  8. <data name="output1" format="fasta"/>
  9. <data name="output2" format="qualsolexa"/>
  10. </outputs>
  11. <tests>
  12. <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
  13. <test>
  14. <param name="input1" value="1.fastqsolexa" ftype="fastqsolexa" />
  15. <output name="output1" file="fastqsolexa_to_fasta_qual_out4.fasta" />
  16. </test>
  17. <test>
  18. <param name="input1" value="2.fastqsolexa" ftype="fastqsolexa" />
  19. <output name="output1" file="fastqsolexa_to_fasta_qual_out2.fasta" />
  20. </test>
  21. </tests>
  22. <help>
  23. .. class:: warningmark
  24. IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64.
  25. -----
  26. **What it does**
  27. This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset.
  28. -----
  29. **Example1**
  30. - Converting the following Solexa fastq data::
  31. @seq1
  32. GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
  33. +seq1
  34. hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
  35. @seq2
  36. GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
  37. +seq2
  38. hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
  39. - will extract the following sequences::
  40. >seq1
  41. GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
  42. >seq2
  43. GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
  44. - and quality scores::
  45. >seq1
  46. 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40
  47. >seq2
  48. 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15
  49. **Example2**
  50. - Converting the following Solexa fastq data::
  51. @HANNIBAL_1_FC302VTAAXX:2:1:228:167
  52. GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
  53. +HANNIBAL_1_FC302VTAAXX:2:1:228:167
  54. 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
  55. @HANNIBAL_1_FC302VTAAXX:2:1:156:340
  56. GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
  57. +HANNIBAL_1_FC302VTAAXX:2:1:156:340
  58. 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
  59. - will extract the following sequences::
  60. >HANNIBAL_1_FC302VTAAXX:2:1:228:167
  61. GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
  62. >HANNIBAL_1_FC302VTAAXX:2:1:156:340
  63. GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
  64. - and quality scores::
  65. >HANNIBAL_1_FC302VTAAXX:2:1:228:167
  66. 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
  67. >HANNIBAL_1_FC302VTAAXX:2:1:156:340
  68. 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
  69. </help>
  70. </tool>