/tools/plotting/scatterplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 71 lines · 43 code · 14 blank · 14 comment · 0 complexity · 9297a8f55a8b7eeac1830e3c75889e64 MD5 · raw file

  1. <tool id="scatterplot_rpy" name="Scatterplot">
  2. <description>of two numeric columns</description>
  3. <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
  4. <inputs>
  5. <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
  6. <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
  7. <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
  8. <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
  9. <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
  10. <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
  11. </inputs>
  12. <outputs>
  13. <data format="pdf" name="out_file1" />
  14. </outputs>
  15. <requirements>
  16. <requirement type="python-module">rpy</requirement>
  17. </requirements>
  18. <!-- TODO: uncomment the following test when we have tools.update_state() working for
  19. multiple dependents with the same dependency.
  20. <tests>
  21. <test>
  22. <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
  23. <param name="col1" value="2"/>
  24. <param name="col2" value="3"/>
  25. <param name="title" value="Scatterplot"/>
  26. <param name="xlab" value="V1"/>
  27. <param name="ylab" value="V2"/>
  28. <output name="out_file1" file="scatterplot_out1.pdf" />
  29. </test>
  30. </tests>
  31. -->
  32. <help>
  33. .. class:: infomark
  34. **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
  35. -----
  36. **Syntax**
  37. This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset.
  38. - All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item.
  39. - **Plot title** The scatterplot title
  40. - **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.
  41. -----
  42. **Example**
  43. - Input file::
  44. 1 68 4.1
  45. 2 71 4.6
  46. 3 62 3.8
  47. 4 75 4.4
  48. 5 58 3.2
  49. 6 60 3.1
  50. 7 67 3.8
  51. 8 68 4.1
  52. 9 71 4.3
  53. 10 69 3.7
  54. - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.
  55. .. image:: ${static_path}/images/scatterplot.png
  56. </help>
  57. </tool>