/tools/fastx_toolkit/fastx_artifacts_filter.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 90 lines · 76 code · 11 blank · 3 comment · 0 complexity · eefbf7eb62b48cc59adbe846862e4e41 MD5 · raw file 

    

  1. <tool id="cshl_fastx_artifacts_filter" name="Remove sequencing artifacts">
    2. 

  2. 	<description></description>
    3. 

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

    4. 

  4. 	<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"
    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="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
    12. 

  12. 

  13. 	</inputs>
    14. 

  14. 

  15. 	<tests>
    16. 

  16. 		<test>
    17. 

  17. 			<!-- Filter FASTA file -->
    18. 

  18. 			<param name="input" value="fastx_artifacts1.fasta" /> 
    19. 

  19. 			<output name="output" file="fastx_artifacts1.out" />
    20. 

  20. 		</test>
    21. 

  21. 		<test>
    22. 

  22. 			<!-- Filter FASTQ file -->
    23. 

  23. 			<param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
    24. 

  24. 			<output name="output" file="fastx_artifacts2.out" />
    25. 

  25. 		</test>
    26. 

  26. 	</tests>
    27. 

  27. 

  28. 	<outputs>
    29. 

  29. 		<data format="input" name="output" metadata_source="input" />
    30. 

  30. 	</outputs>
    31. 

  31. <help>
    32. 

  32. **What it does**
    33. 

  33. 

  34. This tool filters sequencing artifacts (reads with all but 3 identical bases).
    35. 

  35. 

  36. --------
    37. 

  37. 

  38. **The following is an example of sequences which will be filtered out**::
    39. 

  39. 

  40.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    41. 

  41.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    42. 

  42.     AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    43. 

  43.     AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    44. 

  44.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    45. 

  45.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    46. 

  46.     AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA
    47. 

  47.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    48. 

  48.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    49. 

  49.     AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    50. 

  50.     AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    51. 

  51.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    52. 

  52.     CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
    53. 

  53.     AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    54. 

  54.     AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    55. 

  55.     AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
    56. 

  56.     AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    57. 

  57.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
    58. 

  58.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    59. 

  59.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
    60. 

  60.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
    61. 

  61.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
    62. 

  62.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA
    63. 

  63.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA
    64. 

  64.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
    65. 

  65.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA
    66. 

  66.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA
    67. 

  67.     AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    68. 

  68.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
    69. 

  69.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    70. 

  70.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA
    71. 

  71.     AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    72. 

  72.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA
    73. 

  73.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    74. 

  74.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA
    75. 

  75.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA
    76. 

  76.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
    77. 

  77.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    78. 

  78.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    79. 

  79.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA
    80. 

  80.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA
    81. 

  81.     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
    82. 

  82.     
    83. 

  83. ------
    84. 

  84. 

  85. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
    86. 

  86. 

  87.  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    88. 

  88. </help>
    89. 

  89. </tool>
    90. 

  90. <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
    91.