/tools/emboss_5/emboss_tranalign.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 90 lines · 86 code · 4 blank · 0 comment · 0 complexity · ee7b17910fc23c7ab23d397b4071e098 MD5 · raw file

  1. <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
  2. <description>Align nucleic coding regions given the aligned proteins</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Nucleic Sequences</label>
  8. </param>
  9. <param format="data" name="input2" type="data">
  10. <label>Protein Sequences</label>
  11. </param>
  12. <param name="table" type="select">
  13. <label>Code to use</label>
  14. <option value="0">Standard</option>
  15. <option value="1">Standard (with alternative initiation codons)</option>
  16. <option value="2">Vertebrate Mitochondrial</option>
  17. <option value="3">Yeast Mitochondrial</option>
  18. <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
  19. <option value="5">Invertebrate Mitochondrial</option>
  20. <option value="6">Ciliate Macronuclear and Dasycladacean</option>
  21. <option value="9">Echinoderm Mitochondrial</option>
  22. <option value="10">Euplotid Nuclear</option>
  23. <option value="11">Bacterial</option>
  24. <option value="12">Alternative Yeast Nuclear</option>
  25. <option value="13">Ascidian Mitochondrial</option>
  26. <option value="14">Flatworm Mitochondrial</option>
  27. <option value="15">Blepharisma Macronuclear</option>
  28. <option value="16">Chlorophycean Mitochondrial</option>
  29. <option value="21">Trematode Mitochondrial</option>
  30. <option value="22">Scenedesmus obliquus</option>
  31. <option value="23">Thraustochytrium Mitochondrial</option>
  32. </param>
  33. <param name="out_format1" type="select">
  34. <label>Output Sequence File Format</label>
  35. <option value="fasta">FASTA (m)</option>
  36. <option value="acedb">ACeDB (m)</option>
  37. <option value="asn1">ASN.1 (m)</option>
  38. <option value="clustal">Clustal (m)</option>
  39. <option value="codata">CODATA (m)</option>
  40. <option value="embl">EMBL (m)</option>
  41. <option value="fitch">Fitch (m)</option>
  42. <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
  43. <option value="genbank">GENBANK (m)</option>
  44. <option value="gff">GFF (m)</option>
  45. <option value="hennig86">Hennig86 (m)</option>
  46. <option value="ig">Intelligenetics (m)</option>
  47. <option value="jackknifer">Jackknifer (m)</option>
  48. <option value="jackknifernon">Jackknifernon (m)</option>
  49. <option value="mega">Mega (m)</option>
  50. <option value="meganon">Meganon (m)</option>
  51. <option value="msf">Wisconsin Package GCG's MSF (m)</option>
  52. <option value="pir">NBRF (PIR) (m)</option>
  53. <option value="ncbi">NCBI style FASTA (m)</option>
  54. <option value="nexus">Nexus/PAUP (m)</option>
  55. <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
  56. <option value="phylip">PHYLIP interleaved (m)</option>
  57. <option value="phylipnon">PHYLIP non-interleaved (m)</option>
  58. <option value="selex">SELEX (m)</option>
  59. <option value="staden">Staden (s)</option>
  60. <option value="strider">DNA strider (m)</option>
  61. <option value="swiss">SwisProt entry (m)</option>
  62. <option value="text">Plain sequence (s)</option>
  63. <option value="treecon">Treecon (m)</option>
  64. </param>
  65. </inputs>
  66. <outputs>
  67. <data format="fasta" name="out_file1" />
  68. </outputs>
  69. <tests>
  70. <test>
  71. <param name="input1" value="3.fasta"/>
  72. <param name="input2" value="2.pep"/>
  73. <param name="table" value="0"/>
  74. <param name="out_format1" value="fasta"/>
  75. <output name="out_file1" file="emboss_tranalign_out.fasta"/>
  76. </test>
  77. </tests>
  78. <code file="emboss_format_corrector.py" />
  79. <help>
  80. You can view the original documentation here_.
  81. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html
  82. ------
  83. **Citation**
  84. 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;`_
  85. </help>
  86. </tool>