/tools/emboss_5/emboss_prettyseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 59 lines · 51 code · 8 blank · 0 comment · 0 complexity · ab06fc431912cdf50f0a2c4bc7a02d1d MD5 · raw file

  1. <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
  2. <description>Output sequence with translated ranges</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequence</label>
  8. </param>
  9. <param name="ruler" type="select">
  10. <label>Add a ruler</label>
  11. <option value="yes">Yes</option>
  12. <option value="no">No</option>
  13. </param>
  14. <param name="plabel" type="select">
  15. <label>Number translations</label>
  16. <option value="yes">Yes</option>
  17. <option value="no">No</option>
  18. </param>
  19. <param name="nlabel" type="select">
  20. <label>Number DNA sequence</label>
  21. <option value="yes">Yes</option>
  22. <option value="no">No</option>
  23. </param>
  24. <param name="width" size="4" type="text" value="60">
  25. <label>Width of screen</label>
  26. </param>
  27. </inputs>
  28. <outputs>
  29. <data format="prettyseq" name="out_file1" />
  30. </outputs>
  31. <tests>
  32. <test>
  33. <param name="input1" value="2.fasta"/>
  34. <param name="ruler" value="yes"/>
  35. <param name="plabel" value="yes"/>
  36. <param name="nlabel" value="yes"/>
  37. <param name="width" value="60"/>
  38. <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/>
  39. </test>
  40. </tests>
  41. <help>
  42. .. class:: warningmark
  43. The input dataset needs to be sequences.
  44. -----
  45. You can view the original documentation here_.
  46. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyseq.html
  47. ------
  48. **Citation**
  49. 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;`_
  50. </help>
  51. </tool>