/tools/emboss_5/emboss_newseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 78 lines · 74 code · 4 blank · 0 comment · 0 complexity · dfc536b361c3629f86c44f431d4480f5 MD5 · raw file

  1. <tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
  2. <description>Type in a short new sequence</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command>
  5. <inputs>
  6. <param name="seqname" size="10" type="text" value="">
  7. <label>Name of of the sequence</label>
  8. </param>
  9. <param name="description" size="10" type="text" value="">
  10. <label>Description of the sequence</label>
  11. </param>
  12. <param name="type" type="select">
  13. <label>Type of sequence</label>
  14. <option value="N">Nucleic</option>
  15. <option value="P">Protein</option>
  16. </param>
  17. <param name="sequence" size="50" type="text" value="">
  18. <label>The sequence itself</label>
  19. </param>
  20. <param name="out_format1" type="select">
  21. <label>Output Sequence File Format</label>
  22. <option value="fasta">FASTA (m)</option>
  23. <option value="acedb">ACeDB (m)</option>
  24. <option value="asn1">ASN.1 (m)</option>
  25. <option value="clustal">Clustal (m)</option>
  26. <option value="codata">CODATA (m)</option>
  27. <option value="embl">EMBL (m)</option>
  28. <option value="fitch">Fitch (m)</option>
  29. <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
  30. <option value="genbank">GENBANK (m)</option>
  31. <option value="gff">GFF (m)</option>
  32. <option value="hennig86">Hennig86 (m)</option>
  33. <option value="ig">Intelligenetics (m)</option>
  34. <option value="jackknifer">Jackknifer (m)</option>
  35. <option value="jackknifernon">Jackknifernon (m)</option>
  36. <option value="mega">Mega (m)</option>
  37. <option value="meganon">Meganon (m)</option>
  38. <option value="msf">Wisconsin Package GCG's MSF (m)</option>
  39. <option value="pir">NBRF (PIR) (m)</option>
  40. <option value="ncbi">NCBI style FASTA (m)</option>
  41. <option value="nexus">Nexus/PAUP (m)</option>
  42. <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
  43. <option value="phylip">PHYLIP interleaved (m)</option>
  44. <option value="phylipnon">PHYLIP non-interleaved (m)</option>
  45. <option value="selex">SELEX (m)</option>
  46. <option value="staden">Staden (s)</option>
  47. <option value="strider">DNA strider (m)</option>
  48. <option value="swiss">SwisProt entry (m)</option>
  49. <option value="text">Plain sequence (s)</option>
  50. <option value="treecon">Treecon (m)</option>
  51. </param>
  52. </inputs>
  53. <outputs>
  54. <data format="fasta" name="out_file1" />
  55. </outputs>
  56. <tests>
  57. <test>
  58. <param name="seqname" value="cytoc"/>
  59. <param name="description" value="fragment of cytochrome c"/>
  60. <param name="type" value="N"/>
  61. <param name="sequence" value="KKKEERADLIAY"/>
  62. <param name="out_format1" value="fasta"/>
  63. <output name="out_file1" file="emboss_newseq_out.fasta"/>
  64. </test>
  65. </tests>
  66. <code file="emboss_format_corrector.py" />
  67. <help>
  68. You can view the original documentation here_.
  69. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.html
  70. ------
  71. **Citation**
  72. 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;`_
  73. </help>
  74. </tool>