/tools/fastx_toolkit/fastx_renamer.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 65 lines · 45 code · 19 blank · 1 comment · 0 complexity · aca60d780dc0ba6543cf73c890fdebfc MD5 · raw file 

    

  1. <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
    2. 

  2. 	<description></description>
    3. 

  3. 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>

    4. 

  4. 	<command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v 
    5. 

  5. #if $input.ext == "fastqsanger":
    6. 

  6. -Q 33
    7. 

  7. #end if
    8. 

  8. 	</command>
    9. 

  9. 

  10. 	<inputs>
    11. 

  11. 		<param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
    12. 

  12. 

  13. 		<param name="TYPE" type="select" label="Rename sequence identifiers to">
    14. 

  14. 			<option value="SEQ">Nucleotides sequence</option>
    15. 

  15. 			<option value="COUNT">Numeric Counter</option>
    16. 

  16. 		</param>
    17. 

  17. 	</inputs>
    18. 

  18. 

  19. 	<outputs>
    20. 

  20. 		<data format="input" name="output" metadata_source="input" />
    21. 

  21. 	</outputs>
    22. 

  22. 

  23. <help>
    24. 

  24. 

  25. **What it does**
    26. 

  26. 

  27. This tool renames the sequence identifiers in a FASTQ/A file.
    28. 

  28. 

  29. .. class:: infomark
    30. 

  30. 

  31. Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
    32. 

  32. 

  33. --------
    34. 

  34. 

  35. **Example**
    36. 

  36. 

  37. The following Solexa-FASTQ file::
    38. 

  38. 

  39.     @CSHL_4_FC042GAMMII_2_1_517_596
    40. 

  40.     GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
    41. 

  41.     +CSHL_4_FC042GAMMII_2_1_517_596
    42. 

  42.     40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
    43. 

  43.   
    44. 

  44. Renamed to **nucleotides sequence**::
    45. 

  45. 

  46.     @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
    47. 

  47.     GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
    48. 

  48.     +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
    49. 

  49.     40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
    50. 

  50. 

  51. Renamed to **numeric counter**::
    52. 

  52. 

  53.     @1
    54. 

  54.     GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
    55. 

  55.     +1
    56. 

  56.     40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
    57. 

  57. 

  58. ------
    59. 

  59. 

  60. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
    61. 

  61. 

  62.  .. __: http://hannonlab.cshl.edu/fastx_toolkit/   
    63. 

  63. </help>
    64. 

  64. </tool>
    65. 

  65. <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
    66.