/tools/emboss_5/emboss_prettyplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 119 lines · 114 code · 4 blank · 1 comment · 0 complexity · 4b8543d5e7f4ce080db2dab6c2ba4b51 MD5 · raw file

  1. <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
  2. <!-- produces png output with file name -->
  3. <description>Displays aligned sequences, with colouring and boxing</description>
  4. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  5. <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
  6. -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
  7. $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
  8. <inputs>
  9. <param format="data" name="input1" type="data">
  10. <label>Sequence</label>
  11. </param>
  12. <param name="residuesperline" size="10" type="text" value="50">
  13. <label>The number of residues to be displayed on each line</label>
  14. </param>
  15. <param name="resbreak" size="10" type="text" value="50">
  16. <label>Residues before a space</label>
  17. </param>
  18. <param name="ccolours" type="select">
  19. <label>Colour residues by their consensus value</label>
  20. <option value="yes">Yes</option>
  21. <option value="no">No</option>
  22. </param>
  23. <param name="cidentity" size="10" type="text" value="RED">
  24. <label>Colour to display identical residues</label>
  25. </param>
  26. <param name="csimilarity" size="10" type="text" value="GREEN">
  27. <label>Colour to display similar residues</label>
  28. </param>
  29. <param name="cother" size="10" type="text" value="BLACK">
  30. <label>Colour to display other residues</label>
  31. </param>
  32. <param name="docolour" type="select">
  33. <label>Colour residues by table oily, amide etc.</label>
  34. <option value="no">No</option>
  35. <option value="yes">Yes</option>
  36. </param>
  37. <param name="title" type="select">
  38. <label>Display the title</label>
  39. <option value="yes">Yes</option>
  40. <option value="no">No</option>
  41. </param>
  42. <param name="pair" size="10" type="text" value="1.5,1.0,0.5">
  43. <label>Values to represent identical similar related</label>
  44. </param>
  45. <param name="identity" size="10" type="text" value="0">
  46. <label>Only match those which are identical in all sequences</label>
  47. </param>
  48. <param name="box" type="select">
  49. <label>Display prettyboxes</label>
  50. <option value="yes">Yes</option>
  51. <option value="no">No</option>
  52. </param>
  53. <param name="boxcol" type="select">
  54. <label>Colour the background in the boxes</label>
  55. <option value="no">No</option>
  56. <option value="yes">Yes</option>
  57. </param>
  58. <param name="boxcolval" size="10" type="text" value="GREY">
  59. <label>Colour to be used for background</label>
  60. </param>
  61. <param name="name" type="select">
  62. <label>Display the sequence names</label>
  63. <option value="yes">Yes</option>
  64. <option value="no">No</option>
  65. </param>
  66. <param name="maxnamelen" size="10" type="text" value="10">
  67. <label>Margin size for the sequence name</label>
  68. </param>
  69. <param name="number" type="select">
  70. <label>Display the residue number</label>
  71. <option value="yes">Yes</option>
  72. <option value="no">No</option>
  73. </param>
  74. <param name="listoptions" type="select">
  75. <label>Display the date and options used</label>
  76. <option value="yes">Yes</option>
  77. <option value="no">No</option>
  78. </param>
  79. <param name="consensus" type="select">
  80. <label>Display the consensus</label>
  81. <option value="no">No</option>
  82. <option value="yes">Yes</option>
  83. </param>
  84. <param name="collision" type="select">
  85. <label>Allow collisions in calculating consensus</label>
  86. <option value="yes">Yes</option>
  87. <option value="no">No</option>
  88. </param>
  89. <param name="alternative" type="select">
  90. <label>Use alternative collisions routine</label>
  91. <option value="0">Normal collision check</option>
  92. <option value="1">Checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred</option>
  93. <option value="2">If another residue has a greater than or equal to matching score and these do not match then a collision has occurred</option>
  94. <option value="3">Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured</option>
  95. </param>
  96. <param name="showscore" size="10" type="text" value="-1">
  97. <label>Print residue scores</label>
  98. </param>
  99. <param name="portrait" type="select">
  100. <label>Set page to Portrait</label>
  101. <option value="no">No</option>
  102. <option value="yes">Yes</option>
  103. </param>
  104. </inputs>
  105. <outputs>
  106. <data format="png" name="out_file1" />
  107. </outputs>
  108. <help>
  109. You can view the original documentation here_.
  110. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html
  111. ------
  112. **Citation**
  113. 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;`_
  114. </help>
  115. </tool>