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  1. <tool id="rgTDT1" name="Transmission Distortion:">
  2. <description>for family data</description>
  3. <command interpreter="python">
  4. -i '$i.extra_files_path/$i.metadata.base_name' -o '$title'
  5. -r '$out_file1' -l '$logf' -g '$gffout'
  6. </command>
  7. <inputs>
  8. <param name="i" type="data" label="Genotypes for analysis from your current history datasets"
  9. size="132" format="pbed" />
  10. <param name='title' type='text' value='rgTDT' label="Title for the output to remind you what you did" size="80"/>
  11. </inputs>
  12. <outputs>
  13. <data format="tabular" name="out_file1" label="${title}_rgTDT.xls"/>
  14. <data format="gff" name="gffout" label="${title}_rgTDT.gff"/>
  15. <data format="txt" name="logf" label="${title}_rgTDTlog.txt"/>
  16. </outputs>
  17. <tests>
  18. <test>
  19. <param name='i' value='tinywga' ftype='pbed' >
  20. <metadata name='base_name' value='tinywga' />
  21. <composite_data value='tinywga.bim' />
  22. <composite_data value='tinywga.bed' />
  23. <composite_data value='tinywga.fam' />
  24. <edit_attributes type='name' value='tinywga' />
  25. </param>
  26. <param name='title' value='rgTDTtest1' />
  27. <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/>
  28. <output name='gffout' file='rgTDTtest1_TDT_topTable.gff' ftype='gff' compare="diff" />
  29. <output name='logf' file='rgTDTtest1_TDT_log.txt' ftype='txt' lines_diff='79'/>
  30. </test>
  31. </tests>
  32. <help>
  33. .. class:: infomark
  34. **Attribution**
  35. This tool relies on the work of many people. It uses Plink for
  36. analysis, and the R for graphics respectively.
  37. This implementation is a Galaxy tool wrapper around these third party applications.
  38. It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
  39. ross lazarus ( and incorporated into the rgenetics toolkit.
  40. Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy.
  41. -----
  42. .. class:: infomark
  43. **Syntax**
  44. - **Genotype file** is the input family data chosen from available library compressed files
  45. - **Format** determines how your data will be returned to your Galaxy workspace - the gg format is strongly recommended
  46. -----
  47. .. class:: infomark
  48. **Summary**
  49. This tool will perform the standard transmission distortion analyses suitable for
  50. nuclear families and a simple binary "affected" phenotype
  51. If you don't see the genotype data set you want here, it can be imported using one of the methods available from
  52. the Galaxy Get Data tool page.
  53. Outputs will include a GFF toptable with a link to view at UCSC if you want to see your
  54. results as a fully fledged UCSC track.
  55. Finally, if you can't live without
  56. spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited
  57. one with a header. Fortunately excel is dumb enough to open these without much protest.
  58. ----
  59. .. class:: infomark
  60. **Attribution**
  61. This Galaxy tool relies on Plink (see Plinksrc_) to test TDT models.
  62. So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see
  63. DOC_
  64. Tool and Galaxy datatypes originally designed and written for the Rgenetics
  65. series of whole genome scale statistical genetics tools by ross lazarus (
  66. Copyright Ross Lazarus March 2007
  67. This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL.
  68. I'm no lawyer, but it looks like you got GPL if you use this software. Good luck.
  69. .. _Plinksrc:
  70. .. _LGPL:
  71. .. _DOC:
  72. </help>
  73. </tool>