/tools/emboss_5/emboss_pepwheel.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 51 lines · 46 code · 4 blank · 1 comment · 0 complexity · 6e49eb482c8222199f48e86de5d6e7a4 MD5 · raw file

  1. <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
  2. <!-- produces png file -->
  3. <description>Shows protein sequences as helices</description>
  4. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  5. <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
  6. $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
  7. <inputs>
  8. <param format="data" name="input1" type="data">
  9. <label>Sequence</label>
  10. </param>
  11. <param name="steps" size="10" type="text" value="18">
  12. <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label>
  13. </param>
  14. <param name="turns" size="10" type="text" value="5">
  15. <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
  16. </param>
  17. <param name="squares" size="10" type="text" value="ILVM">
  18. <label>Residues to mark with squares</label>
  19. </param>
  20. <param name="diamonds" size="10" type="text" value="DENQST">
  21. <label>Residues to mark with diamonds</label>
  22. </param>
  23. <param name="octags" size="10" type="text" value="HKR">
  24. <label>Residues to mark with octagons</label>
  25. </param>
  26. <param name="wheel" type="select">
  27. <label>Plot the wheel</label>
  28. <option value="yes">Yes</option>
  29. <option value="no">No</option>
  30. </param>
  31. <param name="amphipathic" type="select">
  32. <label>If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified</label>
  33. <option value="no">No</option>
  34. <option value="yes">Yes</option>
  35. </param>
  36. </inputs>
  37. <outputs>
  38. <data format="png" name="out_file1" />
  39. </outputs>
  40. <help>
  41. You can view the original documentation here_.
  42. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html
  43. ------
  44. **Citation**
  45. If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  46. </help>
  47. </tool>