/tools/emboss_5/emboss_helixturnhelix.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 69 lines · 65 code · 4 blank · 0 comment · 0 complexity · 8838b44d2559d3b150118926d1ecfd98 MD5 · raw file

  1. <tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0">
  2. <description>Report nucleic acid binding motifs</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="data" name="input1" type="data">
  7. <label>Sequences</label>
  8. </param>
  9. <param name="mean" size="10" type="text" value="238.71">
  10. <label>Mean value</label>
  11. </param>
  12. <param name="sd" size="10" type="text" value="293.61">
  13. <label>Standard Deviation value</label>
  14. </param>
  15. <param name="minsd" size="10" type="text" value="2.5">
  16. <label>Minimum SD</label>
  17. </param>
  18. <param name="eightyseven" type="select">
  19. <label>Use the old (1987) weight data</label>
  20. <option value="no">No</option>
  21. <option value="yes">Yes</option>
  22. </param>
  23. <param name="out_format1" type="select">
  24. <label>Output Report File Format</label>
  25. <option value="motif">Motif</option>
  26. <option value="embl">EMBL</option>
  27. <option value="genbank">GENBANK</option>
  28. <option value="gff">GFF</option>
  29. <option value="pir">PIR</option>
  30. <option value="swiss">SwissProt</option>
  31. <option value="dbmotif">DbMotif</option>
  32. <option value="diffseq">Diffseq</option>
  33. <option value="excel">Excel (tab delimited)</option>
  34. <option value="feattable">FeatTable</option>
  35. <option value="regions">Regions</option>
  36. <option value="seqtable">SeqTable</option>
  37. <option value="simple">SRS Simple</option>
  38. <option value="srs">SRS</option>
  39. <option value="table">Table</option>
  40. <option value="tagseq">TagSeq</option>
  41. </param>
  42. </inputs>
  43. <outputs>
  44. <data format="motif" name="out_file1" />
  45. </outputs>
  46. <tests>
  47. <test>
  48. <param name="input1" value="2.fasta"/>
  49. <param name="mean" value="238.71"/>
  50. <param name="sd" value="293.61"/>
  51. <param name="minsd" value="2.5"/>
  52. <param name="eightyseven" value="no"/>
  53. <param name="out_format1" value="excel"/>
  54. <output name="out_file1" file="emboss_helixturnhelix_out.tabular"/>
  55. </test>
  56. </tests>
  57. <code file="emboss_format_corrector.py" />
  58. <help>
  59. You can view the original documentation here_.
  60. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.html
  61. ------
  62. **Citation**
  63. 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;`_
  64. </help>
  65. </tool>