/tools/emboss_5/emboss_splitter.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 85 lines · 77 code · 8 blank · 0 comment · 0 complexity · f78264b3bceb6cdcd0ad9d45c5f9d0d2 MD5 · raw file

  1. <tool id="EMBOSS: splitter92" name="splitter" version="5.0.0">
  2. <description>Split a sequence into (overlapping) smaller sequences</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequences</label>
  8. </param>
  9. <param name="size" size="10" type="text" value="10000">
  10. <label>Size to split at</label>
  11. </param>
  12. <param name="overlap" size="4" type="text" value="0">
  13. <label>Overlap between split sequences</label>
  14. </param>
  15. <param name="addoverlap" type="select">
  16. <label>Add overlap to size</label>
  17. <option value="no">No</option>
  18. <option value="yes">Yes</option>
  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="input1" value="2.fasta"/>
  59. <param name="size" value="10000"/>
  60. <param name="overlap" value="0"/>
  61. <param name="addoverlap" value="no"/>
  62. <param name="out_format1" value="fasta"/>
  63. <output name="out_file1" file="emboss_splitter_out.fasta"/>
  64. </test>
  65. </tests>
  66. <code file="emboss_format_corrector.py" />
  67. <help>
  68. .. class:: warningmark
  69. The input dataset needs to be sequences.
  70. -----
  71. You can view the original documentation here_.
  72. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/splitter.html
  73. ------
  74. **Citation**
  75. 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;`_
  76. </help>
  77. </tool>