/tools/emboss_5/emboss_wordmatch.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 80 lines · 61 code · 8 blank · 11 comment · 0 complexity · 490e45a68d84f57b72b3b3f2cbbbc31a 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. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
  5. -offormat5 $out_format3 -auto</command>
  6. <inputs>
  7. <param format="fasta" name="input1" type="data">
  8. <label>Sequence 1</label>
  9. </param>
  10. <param format="fasta" name="input2" type="data">
  11. <label>Sequence 2</label>
  12. </param>
  13. <param name="wordsize" size="5" type="text" value="4">
  14. <label>Word size</label>
  15. </param>
  16. <param name="out_format1" type="select">
  17. <label>Output Alignment File Format</label>
  18. <option value="match">Match (m)</option>
  19. <option value="simple">Simple (m)</option>
  20. <option value="fasta">FASTA (m)</option>
  21. <option value="msf">MSF (m)</option>
  22. <option value="srs">SRS (m)</option>
  23. <option value="pair">Pair (p)</option>
  24. <option value="markx0">Markx0 (p)</option>
  25. <option value="markx1">Markx1 (p)</option>
  26. <option value="markx2">Markx2 (p)</option>
  27. <option value="markx3">Markx3 (p)</option>
  28. <option value="markx10">Markx10 (p)</option>
  29. <option value="srspair">SRS pair (p)</option>
  30. <option value="score">Score (p)</option>
  31. </param>
  32. <param name="out_format2" type="select">
  33. <label>Output Feature 1 File Format</label>
  34. <option value="gff">GFF</option>
  35. <option value="embl">EMBL</option>
  36. <option value="swiss">SwissProt</option>
  37. </param>
  38. <param name="out_format3" type="select">
  39. <label>Output Feature 2 File Format</label>
  40. <option value="gff">GFF</option>
  41. <option value="embl">EMBL</option>
  42. <option value="swiss">SwissProt</option>
  43. </param>
  44. </inputs>
  45. <outputs>
  46. <data format="match" name="out_file1" />
  47. <data format="gff" name="out_file2" />
  48. <data format="gff" name="out_file3" />
  49. </outputs>
  50. <!-- <tests>
  51. <test>
  52. <param name="input1" value="2.fasta"/>
  53. <param name="input2" value="1.fasta"/>
  54. <param name="wordsize" value="4"/>
  55. <param name="out_format1" value="fasta"/>
  56. <param name="out_format2" value="gff"/>
  57. <param name="out_format3" value="gff"/>
  58. <output name="ofile2" file="emboss_wordmatch_out.embl"/>
  59. </test>
  60. </tests> test takes a long time to run-->
  61. <code file="emboss_format_corrector.py" />
  62. <help>
  63. .. class:: warningmark
  64. The input datasets need to be sequences.
  65. -----
  66. You can view the original documentation here_.
  67. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
  68. ------
  69. **Citation**
  70. 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;`_
  71. </help>
  72. </tool>