/tools/genetrack/genetrack_indexer.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 64 lines · 37 code · 21 blank · 6 comment · 0 complexity · ed373ab148854b2c1c114af03ea2ce66 MD5 · raw file

  1. <tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1">
  2. <description>on a BED file</description>
  3. <command interpreter="python">
  4. genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
  5. </command>
  6. <inputs>
  7. <param format="bed6" name="input" type="data" help="Input data">
  8. <label>Select input bed file</label>
  9. </param>
  10. <param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
  11. <label>Shift at 5' end</label>
  12. </param>
  13. <!-- this parameter is currently not used, may not be feasible to use it
  14. <param name="coverage" type="select" label="Full coverage">
  15. <option value="no">NO</option>
  16. <option value="yes">YES</option>
  17. </param>
  18. -->
  19. </inputs>
  20. <outputs>
  21. <data format="genetrack" name="output" />
  22. </outputs>
  23. <help>
  24. **Help**
  25. This tool will create a visualization of the bed file that is selected.
  26. **Parameters**
  27. - **Shift at 5' end** should be used when the location of interest is at a fixed distance from
  28. the 5' end for **all sequenced fragments**!
  29. For example if the sequenced sample consists
  30. mono-nucleosomal DNA (146bp) we should expect that
  31. each nucleosome midpoint is located at 73 bp from the 5' end of the fragment.
  32. Therefore we would enter 73 as the shift parameter. Once corrected the reads
  33. on each strand will coincide and indicate the actual midpoints
  34. of the nucleosomes.
  35. When shifting the averaging process in GeneTrack is able correct for longer or shorter
  36. than expected fragment sizes as long as the errors are reasonably random.
  37. See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
  38. ------
  39. **Citation**
  40. For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. &lt;http://www.ncbi.nlm.nih.gov/pubmed/18388141&gt;`_
  41. If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
  42. </help>
  43. </tool>