/tools/emboss_5/emboss_plotcon.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 28 lines · 23 code · 4 blank · 1 comment · 0 complexity · a326e5409846ae7917a143e801856719 MD5 · raw file

  1. <tool id="EMBOSS: plotcon75" name="plotcon" version="5.0.0">
  2. <!-- produces png file -->
  3. <description>Plot quality of conservation of a sequence alignment</description>
  4. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  5. <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command>
  6. <inputs>
  7. <param format="data" name="input1" type="data">
  8. <label>Sequence</label>
  9. </param>
  10. <param name="winsize" size="10" type="text" value="4">
  11. <label>Number of columns to average alignment quality over</label>
  12. </param>
  13. </inputs>
  14. <outputs>
  15. <data format="png" name="out_file1" />
  16. </outputs>
  17. <help>
  18. You can view the original documentation here_.
  19. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html
  20. ------
  21. **Citation**
  22. 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;`_
  23. </help>
  24. </tool>