/tools/emboss_5/emboss_compseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 48 lines · 41 code · 7 blank · 0 comment · 0 complexity · 54e4b1165168dd9ba410910e6071bb2a MD5 · raw file

  1. <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
  2. <description>Count composition of dimer/trimer/etc words in a sequence</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>On query</label>
  8. </param>
  9. <param name="word" size="4" type="text" value="2">
  10. <label>Size of word (window) to count</label>
  11. </param>
  12. <param name="frame" type="select">
  13. <label>Frame to inspect</label>
  14. <option value="0">All Frames</option>
  15. <option value="1">Frame 1</option>
  16. <option value="2">Frame 2</option>
  17. <option value="3">Frame 3</option>
  18. </param>
  19. </inputs>
  20. <outputs>
  21. <data format="compseq" name="out_file1" />
  22. </outputs>
  23. <tests>
  24. <test>
  25. <param name="input1" value="2.fasta"/>
  26. <param name="word" value="2"/>
  27. <param name="frame" value="0"/>
  28. <output name="out_file1" file="emboss_compseq_out.compseq"/>
  29. </test>
  30. </tests>
  31. <help>
  32. .. class:: warningmark
  33. The input dataset needs to be sequences.
  34. -----
  35. You can view the original documentation here_.
  36. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html
  37. ------
  38. **Citation**
  39. 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;`_
  40. </help>
  41. </tool>