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/tools/plotting/bar_chart.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1. <tool id="barchart_gnuplot" name="Bar chart">
  2. <description>for multiple columns</description>
  3. <command interpreter="python">
  4. #if $xtic.userSpecified == "Yes" #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size"
  5. #else #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size"
  6. #end if
  7. </command>
  8. <inputs>
  9. <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
  10. <conditional name="xtic">
  11. <param name="userSpecified" type="select" label="Use X Tick labels?" help="see example below">
  12. <option value="Yes">Yes</option>
  13. <option value="No">No</option>
  14. </param>
  15. <when value="Yes">
  16. <param name="xticColumn" type="data_column" data_ref="input" numerical="False" label="Use this column for X Tick labels" />
  17. </when>
  18. <when value="No">
  19. </when>
  20. </conditional>
  21. <param name="colList" label="Numerical columns" type="data_column" numerical="True" multiple="True" data_ref="input" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
  22. <param name="title" type="text" size="30" value="Bar Chart" label="Plot title"/>
  23. <param name="ylabel" type="text" size="30" value="V1" label="Label for Y axis"/>
  24. <param name="ymin" type="integer" size="4" value="0" label="Minimal value on Y axis" help="set to 0 for autoscaling"/>
  25. <param name="ymax" type="integer" size="4" value="0" label="Maximal value on Y axis" help="set to 0 for autoscaling"/>
  26. <param name="pdf_size" type="select" label="Choose chart size (pixels)">
  27. <option value="800,600">Normal: 800 by 600</option>
  28. <option value="640,480">Small: 640 by 480</option>
  29. <option value="1480,800">Large: 1480 by 800</option>
  30. <option value="600,800">Normal Flipped: 600 by 800</option>
  31. <option value="480,640">Small Flipped: 480 by 640</option>
  32. <option value="800,1480">Large Flipped: 800 by 1480</option>
  33. </param>
  34. </inputs>
  35. <outputs>
  36. <data format="png" name="out_file1" />
  37. </outputs>
  38. <requirements>
  39. <requirement type="python-module">Gnuplot</requirement>
  40. <requirement type="python-module">Numeric</requirement>
  41. </requirements>
  42. <help>
  43. **What it does**
  44. This tool builds a bar chart on one or more columns. Suppose you have dataset like this one::
  45. Gene1 10 15
  46. Gene2 20 14
  47. Gene3 67 45
  48. Gene4 55 12
  49. Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot:
  50. .. image:: ${static_path}/images/bar_chart.png
  51. :height: 324
  52. :width: 540
  53. </help>
  54. </tool>