/tools/emboss_5/emboss_fuzzpro.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 50 lines · 46 code · 4 blank · 0 comment · 0 complexity · f07d218358e2923ea789683631592ec0 MD5 · raw file

  1. <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0">
  2. <description>Protein pattern search</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="data" name="input1" type="data">
  7. <label>Sequences</label>
  8. </param>
  9. <param name="pattern" size="30" type="text" value="">
  10. <label>Search pattern</label>
  11. </param>
  12. <param name="mismatch" size="5" type="text" value="0">
  13. <label>Number of mismatches</label>
  14. </param>
  15. <param name="out_format1" type="select">
  16. <label>Output Report File Format</label>
  17. <option value="seqtable">SeqTable</option>
  18. <option value="embl">EMBL</option>
  19. <option value="genbank">GENBANK</option>
  20. <option value="gff">GFF</option>
  21. <option value="pir">PIR</option>
  22. <option value="swiss">SwissProt</option>
  23. <option value="dbmotif">DbMotif</option>
  24. <option value="diffseq">Diffseq</option>
  25. <option value="excel">Excel (tab delimited)</option>
  26. <option value="feattable">FeatTable</option>
  27. <option value="motif">Motif</option>
  28. <option value="regions">Regions</option>
  29. <option value="simple">SRS Simple</option>
  30. <option value="srs">SRS</option>
  31. <option value="table">Table</option>
  32. <option value="tagseq">TagSeq</option>
  33. </param>
  34. </inputs>
  35. <outputs>
  36. <data format="fuzzpro" name="out_file1" />
  37. </outputs>
  38. <code file="emboss_format_corrector.py" />
  39. <help>
  40. You can view the original documentation here_.
  41. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html
  42. ------
  43. **Citation**
  44. 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;`_
  45. </help>
  46. </tool>