/tools/emboss_5/emboss_transeq.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 128 lines · 120 code · 8 blank · 0 comment · 0 complexity · 5750776352de454da1c2151e69f010b3 MD5 · raw file

  1. <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
  2. <description>Translate nucleic acid sequences</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
  5. <inputs>
  6. <param format="fasta" name="input1" type="data">
  7. <label>Sequences</label>
  8. </param>
  9. <param name="frame" type="select">
  10. <label>Frame(s) to translate</label>
  11. <option value="1">Frame 1</option>
  12. <option value="2">Frame 2</option>
  13. <option value="3">Frame 3</option>
  14. <option value="F">Forward three frames</option>
  15. <option value="-1">Frame -1</option>
  16. <option value="-2">Frame -2</option>
  17. <option value="-3">Frame -3</option>
  18. <option value="R">Reverse three frames</option>
  19. <option value="6">All six frames</option>
  20. </param>
  21. <param name="table" type="select">
  22. <label>Code to use</label>
  23. <option value="0">Standard</option>
  24. <option value="1">Standard (with alternative initiation codons)</option>
  25. <option value="2">Vertebrate Mitochondrial</option>
  26. <option value="3">Yeast Mitochondrial</option>
  27. <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
  28. <option value="5">Invertebrate Mitochondrial</option>
  29. <option value="6">Ciliate Macronuclear and Dasycladacean</option>
  30. <option value="9">Echinoderm Mitochondrial</option>
  31. <option value="10">Euplotid Nuclear</option>
  32. <option value="11">Bacterial</option>
  33. <option value="12">Alternative Yeast Nuclear</option>
  34. <option value="13">Ascidian Mitochondrial</option>
  35. <option value="14">Flatworm Mitochondrial</option>
  36. <option value="15">Blepharisma Macronuclear</option>
  37. <option value="16">Chlorophycean Mitochondrial</option>
  38. <option value="21">Trematode Mitochondrial</option>
  39. <option value="22">Scenedesmus obliquus</option>
  40. <option value="23">Thraustochytrium Mitochondrial</option>
  41. </param>
  42. <param name="regions" size="10" type="text" value="">
  43. <label>Regions to translate</label>
  44. </param>
  45. <param name="trim" type="select">
  46. <label>Remove all 'X' and '*' characters from the right end of the translation</label>
  47. <option value="no">No</option>
  48. <option value="yes">Yes</option>
  49. </param>
  50. <param name="clean" type="select">
  51. <label>Change all STOP codon positions from the '*' character to 'X'</label>
  52. <option value="no">No</option>
  53. <option value="yes">Yes</option>
  54. </param>
  55. <param name="alternative" type="select">
  56. <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label>
  57. <option value="no">No</option>
  58. <option value="yes">Yes</option>
  59. </param>
  60. <param name="out_format1" type="select">
  61. <label>Output Sequence File Format</label>
  62. <option value="fasta">FASTA (m)</option>
  63. <option value="acedb">ACeDB (m)</option>
  64. <option value="asn1">ASN.1 (m)</option>
  65. <option value="clustal">Clustal (m)</option>
  66. <option value="codata">CODATA (m)</option>
  67. <option value="embl">EMBL (m)</option>
  68. <option value="fitch">Fitch (m)</option>
  69. <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
  70. <option value="genbank">GENBANK (m)</option>
  71. <option value="gff">GFF (m)</option>
  72. <option value="hennig86">Hennig86 (m)</option>
  73. <option value="ig">Intelligenetics (m)</option>
  74. <option value="jackknifer">Jackknifer (m)</option>
  75. <option value="jackknifernon">Jackknifernon (m)</option>
  76. <option value="mega">Mega (m)</option>
  77. <option value="meganon">Meganon (m)</option>
  78. <option value="msf">Wisconsin Package GCG's MSF (m)</option>
  79. <option value="pir">NBRF (PIR) (m)</option>
  80. <option value="ncbi">NCBI style FASTA (m)</option>
  81. <option value="nexus">Nexus/PAUP (m)</option>
  82. <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
  83. <option value="phylip">PHYLIP interleaved (m)</option>
  84. <option value="phylipnon">PHYLIP non-interleaved (m)</option>
  85. <option value="selex">SELEX (m)</option>
  86. <option value="staden">Staden (s)</option>
  87. <option value="strider">DNA strider (m)</option>
  88. <option value="swiss">SwisProt entry (m)</option>
  89. <option value="text">Plain sequence (s)</option>
  90. <option value="treecon">Treecon (m)</option>
  91. </param>
  92. </inputs>
  93. <outputs>
  94. <data format="fasta" name="out_file1" />
  95. </outputs>
  96. <tests>
  97. <test>
  98. <param name="input1" value="2.fasta"/>
  99. <param name="frame" value="1"/>
  100. <param name="table" value="0"/>
  101. <param name="regions" value=""/>
  102. <param name="trim" value="no"/>
  103. <param name="clean" value="no"/>
  104. <param name="alternative" value="no"/>
  105. <param name="out_format1" value="fasta"/>
  106. <output name="out_file1" file="emboss_transeq_out.fasta"/>
  107. </test>
  108. </tests>
  109. <code file="emboss_format_corrector.py" />
  110. <help>
  111. .. class:: warningmark
  112. The input dataset needs to be sequences.
  113. -----
  114. You can view the original documentation here_.
  115. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html
  116. ------
  117. **Citation**
  118. 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;`_
  119. </help>
  120. </tool>