/tools/emboss_5/emboss_fuzztran.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 101 lines · 93 code · 8 blank · 0 comment · 0 complexity · 7ddd4269ac0177d4ca83453a506f6a91 MD5 · raw file

  1. <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
  2. <description>Protein pattern search after translation</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequences</label>
  8. </param>
  9. <param name="pattern" size="5" 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="frame" type="select">
  16. <label>Frame(s) to translate</label>
  17. <option value="1">Frame 1</option>
  18. <option value="2">Frame 2</option>
  19. <option value="3">Frame 3</option>
  20. <option value="F">Forward three frames</option>
  21. <option value="-1">Frame -1</option>
  22. <option value="-2">Frame -2</option>
  23. <option value="-3">Frame -3</option>
  24. <option value="R">Reverse three frames</option>
  25. <option value="6">All six frames</option>
  26. </param>
  27. <param name="table" type="select">
  28. <label>Code to use</label>
  29. <option value="0">Standard</option>
  30. <option value="1">Standard (with alternative initiation codons)</option>
  31. <option value="2">Vertebrate Mitochondrial</option>
  32. <option value="3">Yeast Mitochondrial</option>
  33. <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
  34. <option value="5">Invertebrate Mitochondrial</option>
  35. <option value="6">Ciliate Macronuclear and Dasycladacean</option>
  36. <option value="9">Echinoderm Mitochondrial</option>
  37. <option value="10">Euplotid Nuclear</option>
  38. <option value="11">Bacterial</option>
  39. <option value="12">Alternative Yeast Nuclear</option>
  40. <option value="13">Ascidian Mitochondrial</option>
  41. <option value="14">Flatworm Mitochondrial</option>
  42. <option value="15">Blepharisma Macronuclear</option>
  43. <option value="16">Chlorophycean Mitochondrial</option>
  44. <option value="21">Trematode Mitochondrial</option>
  45. <option value="22">Scenedesmus obliquus</option>
  46. <option value="23">Thraustochytrium Mitochondrial</option>
  47. </param>
  48. <param name="out_format1" type="select">
  49. <label>Output Report File Format</label>
  50. <option value="table">Table</option>
  51. <option value="embl">EMBL</option>
  52. <option value="genbank">GENBANK</option>
  53. <option value="gff">GFF</option>
  54. <option value="pir">PIR</option>
  55. <option value="swiss">SwissProt</option>
  56. <option value="dbmotif">DbMotif</option>
  57. <option value="diffseq">Diffseq</option>
  58. <option value="excel">Excel (tab delimited)</option>
  59. <option value="feattable">FeatTable</option>
  60. <option value="motif">Motif</option>
  61. <option value="regions">Regions</option>
  62. <option value="seqtable">SeqTable</option>
  63. <option value="simple">SRS Simple</option>
  64. <option value="srs">SRS</option>
  65. <option value="tagseq">TagSeq</option>
  66. </param>
  67. </inputs>
  68. <outputs>
  69. <data format="fuzztran" name="out_file1" />
  70. </outputs>
  71. <tests>
  72. <test>
  73. <param name="input1" value="1.fasta"/>
  74. <param name="pattern" value="AA"/>
  75. <param name="mismatch" value="0"/>
  76. <param name="frame" value="6"/>
  77. <param name="table" value="0"/>
  78. <param name="out_format1" value="excel"/>
  79. <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
  80. </test>
  81. </tests>
  82. <code file="emboss_format_corrector.py" />
  83. <help>
  84. .. class:: warningmark
  85. The input dataset needs to be sequences.
  86. -----
  87. You can view the original documentation here_.
  88. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html
  89. ------
  90. **Citation**
  91. 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;`_
  92. </help>
  93. </tool>