/tools/emboss_5/emboss_textsearch.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 64 lines · 60 code · 4 blank · 0 comment · 0 complexity · 680bfe046d77e4a400e1296b24b3a6fb MD5 · raw file

  1. <tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
  2. <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
  5. $html_out1 -auto</command>
  6. <inputs>
  7. <param format="data" name="input1" type="data">
  8. <label>Sequence</label>
  9. </param>
  10. <param name="pattern" size="50" type="text" value="">
  11. <label>Pattern to search for</label>
  12. </param>
  13. <param name="casesensitive" type="select">
  14. <label>Do a case-sensitive search</label>
  15. <option value="no">No</option>
  16. <option value="yes">Yes</option>
  17. </param>
  18. <param name="heading" type="select">
  19. <label>Display column headings</label>
  20. <option value="yes">Yes</option>
  21. <option value="no">No</option>
  22. </param>
  23. <param name="usa" type="select">
  24. <label>Display the USA of the sequence</label>
  25. <option value="yes">Yes</option>
  26. <option value="no">No</option>
  27. </param>
  28. <param name="accession" type="select">
  29. <label>Display accession column</label>
  30. <option value="yes">Yes</option>
  31. <option value="no">No</option>
  32. </param>
  33. <param name="search_name" type="select">
  34. <label>Display name column</label>
  35. <option value="yes">Yes</option>
  36. <option value="no">No</option>
  37. </param>
  38. <param name="description" type="select">
  39. <label>Display description column</label>
  40. <option value="yes">Yes</option>
  41. <option value="no">No</option>
  42. </param>
  43. <param name="html_out1" type="select">
  44. <label>Format output as an HTML table</label>
  45. <option value="no">No</option>
  46. <option value="yes">Yes</option>
  47. </param>
  48. </inputs>
  49. <outputs>
  50. <data format="textsearch" name="out_file1" />
  51. </outputs>
  52. <code file="emboss_format_corrector.py" />
  53. <help>
  54. You can view the original documentation here_.
  55. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html
  56. ------
  57. **Citation**
  58. 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;`_
  59. </help>
  60. </tool>