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/tools/emboss_5/emboss_revseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1. <tool id="EMBOSS: revseq82" name="revseq" version="5.0.0">
  2. <description>Reverse and complement a sequence</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequences</label>
  8. </param>
  9. <param name="reverse" type="select">
  10. <label>Reverse the sequence</label>
  11. <option value="yes">Yes</option>
  12. <option value="no">No</option>
  13. </param>
  14. <param name="complement" type="select">
  15. <label>Complement the sequence</label>
  16. <option value="yes">Yes</option>
  17. <option value="no">No</option>
  18. </param>
  19. <param name="out_format1" type="select">
  20. <label>Output Sequence File Format</label>
  21. <option value="fasta">FASTA (m)</option>
  22. <option value="acedb">ACeDB (m)</option>
  23. <option value="asn1">ASN.1 (m)</option>
  24. <option value="clustal">Clustal (m)</option>
  25. <option value="codata">CODATA (m)</option>
  26. <option value="embl">EMBL (m)</option>
  27. <option value="fitch">Fitch (m)</option>
  28. <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
  29. <option value="genbank">GENBANK (m)</option>
  30. <option value="gff">GFF (m)</option>
  31. <option value="hennig86">Hennig86 (m)</option>
  32. <option value="ig">Intelligenetics (m)</option>
  33. <option value="jackknifer">Jackknifer (m)</option>
  34. <option value="jackknifernon">Jackknifernon (m)</option>
  35. <option value="mega">Mega (m)</option>
  36. <option value="meganon">Meganon (m)</option>
  37. <option value="msf">Wisconsin Package GCG's MSF (m)</option>
  38. <option value="pir">NBRF (PIR) (m)</option>
  39. <option value="ncbi">NCBI style FASTA (m)</option>
  40. <option value="nexus">Nexus/PAUP (m)</option>
  41. <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
  42. <option value="phylip">PHYLIP interleaved (m)</option>
  43. <option value="phylipnon">PHYLIP non-interleaved (m)</option>
  44. <option value="selex">SELEX (m)</option>
  45. <option value="staden">Staden (s)</option>
  46. <option value="strider">DNA strider (m)</option>
  47. <option value="swiss">SwisProt entry (m)</option>
  48. <option value="text">Plain sequence (s)</option>
  49. <option value="treecon">Treecon (m)</option>
  50. </param>
  51. </inputs>
  52. <outputs>
  53. <data format="fasta" name="out_file1" />
  54. </outputs>
  55. <tests>
  56. <test>
  57. <param name="input1" value="2.fasta"/>
  58. <param name="reverse" value="yes"/>
  59. <param name="complement" value="yes"/>
  60. <param name="out_format1" value="fasta"/>
  61. <output name="out_file1" file="emboss_revseq_out.fasta"/>
  62. </test>
  63. </tests>
  64. <code file="emboss_format_corrector.py" />
  65. <help>
  66. .. class:: warningmark
  67. The input dataset needs to be sequences.
  68. -----
  69. You can view the original documentation here_.
  70. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/revseq.html
  71. ------
  72. **Citation**
  73. 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;`_
  74. </help>
  75. </tool>