/tools/emboss_5/emboss_primersearch.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 39 lines · 34 code · 5 blank · 0 comment · 0 complexity · 22aeb319314bc07d8e0beed235a8e7b1 MD5 · raw file

  1. <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
  2. <description>Searches DNA sequences for matches with primer pairs</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Main sequences</label>
  8. </param>
  9. <param format="data" name="input2" type="data">
  10. <label>Primer file</label>
  11. </param>
  12. <param name="mismatchpercent" size="4" type="text" value="0">
  13. <label>Allowed percent mismatch</label>
  14. </param>
  15. </inputs>
  16. <outputs>
  17. <data format="primersearch" name="out_file1" />
  18. </outputs>
  19. <tests>
  20. <test>
  21. <param name="input1" value="2.fasta"/>
  22. <param name="input2" value="emboss_primersearch.fasta"/>
  23. <param name="mismatchpercent" value="0"/>
  24. <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
  25. </test>
  26. </tests>
  27. <help>
  28. You can view the original documentation here_.
  29. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
  30. ------
  31. **Citation**
  32. 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;`_
  33. </help>
  34. </tool>