/tools/human_genome_variation/funDo.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 101 lines · 76 code · 25 blank · 0 comment · 0 complexity · 35be3a9b20bbbcbbb3b1059d39e4dc71 MD5 · raw file

  1. <tool id="hgv_funDo" name="FunDO" version="1.0.0">
  2. <description>human genes associated with disease terms</description>
  3. <command interpreter="perl">
  4. disease_ontology_gene_fuzzy_selector.pl $build $out_file1 ${GALAXY_DATA_INDEX_DIR}/funDo.loc '$term'
  5. </command>
  6. <inputs>
  7. <param name="build" type="select" label="Database build">
  8. <options from_file="funDo.loc">
  9. <column name="name" index="0"/>
  10. <column name="value" index="0"/>
  11. <filter type="unique_value" column="0"/>
  12. </options>
  13. </param>
  14. <param name="term" size="40" type="text" label="Disease term(s)" />
  15. </inputs>
  16. <outputs>
  17. <data format="interval" name="out_file1">
  18. </data>
  19. </outputs>
  20. <tests>
  21. <test>
  22. <param name="term" value="lung"/>
  23. <param name="build" value="hg18"/>
  24. <output name="out_file1" file="funDo_output1.interval" />
  25. </test>
  26. </tests>
  27. <help>
  28. **Dataset formats**
  29. There is no input dataset. The output is in interval_ format.
  30. .. _interval: ./static/formatHelp.html#interval
  31. -----
  32. **What it does**
  33. This tool searches the disease-term field of the DOLite mappings
  34. used by the FunDO project and returns a set of genes that
  35. are associated with terms matching the specified pattern. (This is the
  36. reverse of what FunDO's own server does.)
  37. The search is case insensitive, and selects terms that contain any of
  38. the given words, either exactly or within a longer word (e.g. "nemia"
  39. selects not only "anemia", but also "hyperglycinemia", "tyrosinemias",
  40. and many other things). Multiple words should be separated by spaces,
  41. not commas. As a special case, entering the word "disease" returns all
  42. genes associated with any disease, even if that word does not actually
  43. appear in the term field.
  44. Website: http://django.nubic.northwestern.edu/fundo/
  45. -----
  46. **Example**
  47. Typing::
  48. carcinoma
  49. results in::
  50. 1. 2. 3. 4. 5. 6. 7.
  51. chr11 89507465 89565427 + NAALAD2 10003 Adenocarcinoma
  52. chr15 50189113 50192264 - BCL2L10 10017 Carcinoma
  53. chr7 150535855 150555250 - ABCF2 10061 Clear cell carcinoma
  54. chr7 150540508 150555250 - ABCF2 10061 Clear cell carcinoma
  55. chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma
  56. chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma
  57. etc.
  58. where the column contents are as follows::
  59. 1. chromosome name
  60. 2. start position of the gene
  61. 3. end position of the gene
  62. 4. strand
  63. 4. gene name
  64. 6. Entrez Gene ID
  65. 7. disease term
  66. -----
  67. **References**
  68. Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. (2009)
  69. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose
  70. ontology for the test of gene-ontology associations.
  71. Bioinformatics. 25(12):i63-8.
  72. Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. (2009)
  73. Annotating the human genome with Disease Ontology.
  74. BMC Genomics. 10 Suppl 1:S6.
  75. </help>
  76. </tool>