/tools/emboss_5/emboss_dan.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 90 lines · 66 code · 4 blank · 20 comment · 0 complexity · 5aa0ef0dcac230aeca3b5a59919fda33 MD5 · raw file

  1. <tool id="EMBOSS: dan19" name="dan" version="5.0.0">
  2. <description>Calculates DNA RNA/DNA melting temperature</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
  5. -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
  6. <inputs>
  7. <param format="data" name="input1" type="data">
  8. <label>On query</label>
  9. </param>
  10. <param name="window" size="4" type="text" value="20">
  11. <label>Window Size</label>
  12. </param>
  13. <param name="shift" size="4" type="text" value="1">
  14. <label>Step size (shift increment)</label>
  15. </param>
  16. <param name="dnaconc" size="4" type="text" value="50.0">
  17. <label>DNA Concentration (nM)</label>
  18. </param>
  19. <param name="saltconc" size="4" type="text" value="50.0">
  20. <label>Salt concentration (mM)</label>
  21. </param>
  22. <param name="thermo" type="select">
  23. <label>Output the DeltaG, DeltaH and DeltaS values</label>
  24. <option value="yes">Yes</option>
  25. <option value="no">No</option>
  26. </param>
  27. <param name="temperature" size="4" type="text" value="25 ">
  28. <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
  29. </param>
  30. <param name="rna" type="select">
  31. <label>Sequence is RNA</label>
  32. <option value="no">No</option>
  33. <option value="yes">Yes</option>
  34. </param>
  35. <param name="product" type="select">
  36. <label>Include percent formamide, percent of mismatches allowed and product length</label>
  37. <option value="no">No</option>
  38. <option value="yes">Yes</option>
  39. </param>
  40. <param name="formamide" size="4" type="text" value="0 ">
  41. <label>Formamide concentration (nM)</label>
  42. </param>
  43. <param name="mismatch" size="4" type="text" value="0 ">
  44. <label>Percent mismatch to be used in calculations</label>
  45. </param>
  46. <param name="prodlen" size="4" type="text" value="20">
  47. <label>Product length to be used in calculations</label>
  48. </param>
  49. <param name="plot1" type="select">
  50. <label>Create a graph</label>
  51. <option value="no">No</option>
  52. <option value="yes">Yes</option>
  53. </param>
  54. </inputs>
  55. <outputs>
  56. <data format="dan" name="out_file1" />
  57. </outputs>
  58. <!--
  59. <tests>
  60. <test>
  61. <param name="input1" value="2.fasta"/>
  62. <param name="window" value="20"/>
  63. <param name="shift" value="1"/>
  64. <param name="dnaconc" value="50"/>
  65. <param name="saltconc" value="50"/>
  66. <param name="thermo" value="yes"/>
  67. <param name="temperature" value="25"/>
  68. <param name="rna" value="no"/>
  69. <param name="product" value="no"/>
  70. <param name="formamide" value="0"/>
  71. <param name="mismatch" value="0"/>
  72. <param name="prodlen" value="20"/>
  73. <param name="plot1" value="yes"/>
  74. <output name="out_file1" file="emboss_dan_out.png"/>
  75. </test>
  76. </tests>
  77. -->
  78. <code file="emboss_format_corrector.py" />
  79. <help>
  80. You can view the original documentation here_.
  81. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html
  82. ------
  83. **Citation**
  84. 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;`_
  85. </help>
  86. </tool>