/tools/emboss_5/emboss_newcpgseek.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 41 lines · 33 code · 8 blank · 0 comment · 0 complexity · c81417176f58dd837bbb6373187557b4 MD5 · raw file

  1. <tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0">
  2. <description>Reports CpG rich region</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequence</label>
  8. </param>
  9. <param name="score" size="4" type="text" value="17">
  10. <label>CpG score</label>
  11. </param>
  12. </inputs>
  13. <outputs>
  14. <data format="newcpgseek" name="out_file1" />
  15. </outputs>
  16. <tests>
  17. <test>
  18. <param name="input1" value="2.fasta"/>
  19. <param name="score" value="17"/>
  20. <output name="out_file1" file="emboss_newcpgseek_out.newcpgseek"/>
  21. </test>
  22. </tests>
  23. <help>
  24. .. class:: warningmark
  25. The input dataset needs to be sequences.
  26. -----
  27. You can view the original documentation here_.
  28. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgseek.html
  29. ------
  30. **Citation**
  31. 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;`_
  32. </help>
  33. </tool>