/tools/taxonomy/t2t_report.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 72 lines · 57 code · 15 blank · 0 comment · 0 complexity · f71314c963079098ff6190e4d64e6fe6 MD5 · raw file

  1. <tool id="t2t_report" name="Summarize taxonomy" version="1.0.0">
  2. <description></description>
  3. <requirements>
  4. <requirement type="package">taxonomy</requirement>
  5. </requirements>
  6. <command>taxonomy2tree $input 0 /dev/null $out_file1 0</command>
  7. <inputs>
  8. <param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/>
  9. </inputs>
  10. <outputs>
  11. <data format="tabular" name="out_file1" />
  12. </outputs>
  13. <requirements>
  14. <requirement type="binary">taxonomy2tree</requirement>
  15. </requirements>
  16. <tests>
  17. <test>
  18. <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
  19. <output name="out_file1" file="t2t_report.tabular"/>
  20. </test>
  21. </tests>
  22. <help>
  23. **What it does**
  24. Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks.
  25. ------
  26. **Example**
  27. Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
  28. 9916 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n
  29. 9606 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n
  30. Running this tool will generate the following output::
  31. Rank Rank Name Count
  32. -------------------------------------
  33. root root 2
  34. superkingdom Eukaryota 2
  35. kingdom Metazoa 2
  36. phylum Chordata 2
  37. subphylum Craniata 2
  38. superclass Gnathostomata 2
  39. class Mammalia 2
  40. superorder Euarchontoglires 1
  41. superorder Laurasiatheria 1
  42. order Primates 1
  43. suborder Haplorrhini 1
  44. suborder Ruminantia 1
  45. superfamily Hominoidea 1
  46. family Bovidae 1
  47. family Hominidae 1
  48. subfamily Bovinae 1
  49. genus Bos 1
  50. genus Homo 1
  51. species Bos taurus 1
  52. species Homo sapiens 1
  53. The output is sorted on Rank and then on Rank Name.
  54. .. class:: warningmark
  55. **Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not.
  56. </help>
  57. </tool>