/tools/fastx_toolkit/fastx_trimmer.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 81 lines · 59 code · 19 blank · 3 comment · 0 complexity · cde5be9e5f1db725d1ee243223867788 MD5 · raw file 

    

  1. <tool id="cshl_fastx_trimmer" name="Trim sequences">
    2. 

  2. 	<description></description>
    3. 

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

    4. 

  4. 	<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -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,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
    12. 

  12. 

  13. 		<param name="first" size="4" type="integer" value="1">
    14. 

  14. 			<label>First base to keep</label>
    15. 

  15. 		</param>
    16. 

  16. 

  17. 		<param name="last" size="4" type="integer" value="21">
    18. 

  18. 			<label>Last base to keep</label>
    19. 

  19. 		</param>
    20. 

  20. 	</inputs>
    21. 

  21. 

  22. 	<tests>
    23. 

  23. 		<test>
    24. 

  24. 			<!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
    25. 

  25. 			<param name="input" value="fastx_trimmer1.fasta" />
    26. 

  26. 			<param name="first" value="5"/>
    27. 

  27. 			<param name="last" value="36"/>
    28. 

  28. 			<output name="output" file="fastx_trimmer1.out" />
    29. 

  29. 		</test>
    30. 

  30. 		<test>
    31. 

  31. 			<!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
    32. 

  32. 			<param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
    33. 

  33. 			<param name="first" value="1"/>
    34. 

  34. 			<param name="last" value="27"/>
    35. 

  35. 			<output name="output" file="fastx_trimmer2.out" />
    36. 

  36. 		</test>
    37. 

  37. 	</tests>
    38. 

  38. 

  39. 	<outputs>
    40. 

  40. 		<data format="input" name="output" metadata_source="input" />
    41. 

  41. 	</outputs>
    42. 

  42. 	<help>
    43. 

  43. **What it does**
    44. 

  44. 

  45. This tool trims (cut bases from) sequences in a FASTA/Q file.
    46. 

  46.   
    47. 

  47. --------
    48. 

  48. 

  49. **Example**
    50. 

  50. 

  51. Input Fasta file (with 36 bases in each sequences)::
    52. 

  52. 

  53.     >1-1
    54. 

  54.     TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
    55. 

  55.     >2-1
    56. 

  56.     CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
    57. 

  57.     
    58. 

  58. 

  59. Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
    60. 

  60. 

  61.     >1-1
    62. 

  62.     TATGGTCAGAAACCATATGCA
    63. 

  63.     >2-1
    64. 

  64.     CAGCGAGGCTTTAATGCCATT
    65. 

  65. 

  66. Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
    67. 

  67. 

  68.     >1-1
    69. 

  69.     TCAGA
    70. 

  70.     >2-1
    71. 

  71.     AGGCT
    72. 

  72.     
    73. 

  73.     ------
    74. 

  74. 

  75. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
    76. 

  76. 

  77.  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    78. 

  78.     
    79. 

  79. </help>
    80. 

  80. </tool>
    81. 

  81. <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
    82.