/tools/regVariation/substitution_rates.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 61 lines · 50 code · 11 blank · 0 comment · 0 complexity · 199b18379b2600b9b894ca82e48cecbe MD5 · raw file

  1. <tool id="subRate1" name="Estimate substitution rates " version="1.0.0">
  2. <description> for non-coding regions</description>
  3. <command interpreter="python">
  4. substitution_rates.py
  5. $input
  6. $out_file1
  7. #if $region.type == "win":
  8. ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol
  9. #else:
  10. "None"
  11. #end if
  12. </command>
  13. <inputs>
  14. <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
  15. <conditional name="region">
  16. <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
  17. <option value="align">Alignment block</option>
  18. <option value="win">Intervals in your history</option>
  19. </param>
  20. <when value="win">
  21. <param format="interval" name="input2" type="data" label="Choose intervals">
  22. <validator type="unspecified_build" />
  23. </param>
  24. </when>
  25. <when value="align" />
  26. </conditional>
  27. </inputs>
  28. <outputs>
  29. <data format="tabular" name="out_file1" metadata_source="input"/>
  30. </outputs>
  31. <tests>
  32. <test>
  33. <param name="input" value="Interval2Maf_pairwise_out.maf"/>
  34. <param name="type" value="align"/>
  35. <output name="out_file1" file="subRates1.out"/>
  36. </test>
  37. </tests>
  38. <help>
  39. .. class:: infomark
  40. **What it does**
  41. This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explained below:
  42. - L: number of nucleotides compared
  43. - N: number of different nucleotides
  44. - p = N/L
  45. -----
  46. .. class:: warningmark
  47. **Note**
  48. Any block/s not containing exactly two sequences, will be omitted.
  49. </help>
  50. </tool>