/tools/filters/wiggle_to_simple.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 88 lines · 73 code · 15 blank · 0 comment · 0 complexity · 0cfad6cec2abdaa4c863cc1a7062c0a6 MD5 · raw file

  1. <tool id="wiggle2simple1" name="Wiggle-to-Interval">
  2. <description>converter</description>
  3. <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
  4. <inputs>
  5. <param format="wig" name="input" type="data" label="Convert"/>
  6. </inputs>
  7. <outputs>
  8. <data format="interval" name="out_file1" />
  9. </outputs>
  10. <tests>
  11. <test>
  12. <param name="input" value="2.wig" />
  13. <output name="out_file1" file="2.interval"/>
  14. </test>
  15. <test>
  16. <param name="input" value="3.wig" />
  17. <output name="out_file1" file="3_wig.bed"/>
  18. </test>
  19. </tests>
  20. <help>
  21. **Syntax**
  22. This tool converts wiggle data into interval type.
  23. - **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below.
  24. - **BED format** with no declaration line and four columns of data::
  25. chromA chromStartA chromEndA dataValueA
  26. chromB chromStartB chromEndB dataValueB
  27. - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
  28. variableStep chrom=chrN [span=windowSize]
  29. chromStartA dataValueA
  30. chromStartB dataValueB
  31. - **fixedStep** single column data; started by a declaration line and followed with data values::
  32. fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
  33. dataValue1
  34. dataValue2
  35. -----
  36. **Example**
  37. - input wiggle format file::
  38. #track type=wiggle_0 name="Bed Format" description="BED format"
  39. chr19 59302000 59302300 -1.0
  40. chr19 59302300 59302600 -0.75
  41. chr19 59302600 59302900 -0.50
  42. chr19 59302900 59303200 -0.25
  43. chr19 59303200 59303500 0.0
  44. #track type=wiggle_0 name="variableStep" description="variableStep format"
  45. variableStep chrom=chr19 span=150
  46. 59304701 10.0
  47. 59304901 12.5
  48. 59305401 15.0
  49. 59305601 17.5
  50. #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
  51. fixedStep chrom=chr19 start=59307401 step=300 span=200
  52. 1000
  53. 900
  54. 800
  55. 700
  56. 600
  57. - convert the above file to interval file::
  58. chr19 59302000 59302300 + -1.0
  59. chr19 59302300 59302600 + -0.75
  60. chr19 59302600 59302900 + -0.5
  61. chr19 59302900 59303200 + -0.25
  62. chr19 59303200 59303500 + 0.0
  63. chr19 59304701 59304851 + 10.0
  64. chr19 59304901 59305051 + 12.5
  65. chr19 59305401 59305551 + 15.0
  66. chr19 59305601 59305751 + 17.5
  67. chr19 59307701 59307901 + 1000.0
  68. chr19 59308001 59308201 + 900.0
  69. chr19 59308301 59308501 + 800.0
  70. chr19 59308601 59308801 + 700.0
  71. chr19 59308901 59309101 + 600.0
  72. </help>
  73. </tool>