/tools/emboss_5/emboss_wordmatch.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 73 lines · 57 code · 5 blank · 11 comment · 0 complexity · 01b80e4f677aebe997be8f7924f8a356 MD5 · raw file

  1. <tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
  2. <description>Finds all exact matches of a given size between 2 sequences</description>
  3. <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
  4. -offormat5 $out_format3 -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequence 1</label>
  8. </param>
  9. <param format="fasta" name="input2" type="data">
  10. <label>Sequence 2</label>
  11. </param>
  12. <param name="wordsize" size="5" type="text" value="4">
  13. <label>Word size</label>
  14. </param>
  15. <param name="out_format1" type="select">
  16. <label>Output Alignment File Format</label>
  17. <option value="match">Match (m)</option>
  18. <option value="simple">Simple (m)</option>
  19. <option value="fasta">FASTA (m)</option>
  20. <option value="msf">MSF (m)</option>
  21. <option value="srs">SRS (m)</option>
  22. <option value="pair">Pair (p)</option>
  23. <option value="markx0">Markx0 (p)</option>
  24. <option value="markx1">Markx1 (p)</option>
  25. <option value="markx2">Markx2 (p)</option>
  26. <option value="markx3">Markx3 (p)</option>
  27. <option value="markx10">Markx10 (p)</option>
  28. <option value="srspair">SRS pair (p)</option>
  29. <option value="score">Score (p)</option>
  30. </param>
  31. <param name="out_format2" type="select">
  32. <label>Output Feature 1 File Format</label>
  33. <option value="gff">GFF</option>
  34. <option value="embl">EMBL</option>
  35. <option value="swiss">SwissProt</option>
  36. </param>
  37. <param name="out_format3" type="select">
  38. <label>Output Feature 2 File Format</label>
  39. <option value="gff">GFF</option>
  40. <option value="embl">EMBL</option>
  41. <option value="swiss">SwissProt</option>
  42. </param>
  43. </inputs>
  44. <outputs>
  45. <data format="match" name="out_file1" />
  46. <data format="gff" name="out_file2" />
  47. <data format="gff" name="out_file3" />
  48. </outputs>
  49. <!-- <tests>
  50. <test>
  51. <param name="input1" value="2.fasta"/>
  52. <param name="input2" value="1.fasta"/>
  53. <param name="wordsize" value="4"/>
  54. <param name="out_format1" value="fasta"/>
  55. <param name="out_format2" value="gff"/>
  56. <param name="out_format3" value="gff"/>
  57. <output name="ofile2" file="emboss_wordmatch_out.embl"/>
  58. </test>
  59. </tests> test takes a long time to run-->
  60. <code file="emboss_format_corrector.py" />
  61. <help>
  62. .. class:: warningmark
  63. The input datasets need to be sequences.
  64. -----
  65. You can view the original documentation here_.
  66. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
  67. </help>
  68. </tool>