/tools/emboss_5/emboss_einverted.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 49 lines · 45 code · 4 blank · 0 comment · 0 complexity · 33c7f16d7050bb725685d1c13b65c0b2 MD5 · raw file

  1. <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
  2. <description>Finds DNA inverted repeats</description>
  3. <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
  4. <inputs>
  5. <param format="fasta" name="input1" type="data">
  6. <label>On query</label>
  7. </param>
  8. <param name="gap" size="4" type="text" value="12">
  9. <label>Gap penalty</label>
  10. </param>
  11. <param name="threshold" size="4" type="text" value="50">
  12. <label>Minimum score threshold</label>
  13. </param>
  14. <param name="match" size="4" type="text" value="3">
  15. <label>Match score</label>
  16. </param>
  17. <param name="mismatch" size="4" type="text" value="-4">
  18. <label>Mismatch score</label>
  19. </param>
  20. <param name="maxrepeat" size="4" type="text" value="2000">
  21. <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
  22. </param>
  23. </inputs>
  24. <outputs>
  25. <data format="einverted" name="out_file1" />
  26. </outputs>
  27. <tests>
  28. <test>
  29. <param name="input1" value="1.fasta"/>
  30. <param name="gap" value="12"/>
  31. <param name="threshold" value="50"/>
  32. <param name="match" value="3"/>
  33. <param name="mismatch" value="-4"/>
  34. <param name="maxrepeat" value="2000"/>
  35. <output name="out_file1" file="emboss_einverted_out.einverted"/>
  36. </test>
  37. </tests>
  38. <help>
  39. .. class:: warningmark
  40. The input dataset needs to be sequences.
  41. -----
  42. You can view the original documentation here_.
  43. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
  44. </help>
  45. </tool>