/tools/solid_tools/solid_qual_boxplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 40 lines · 25 code · 15 blank · 0 comment · 0 complexity · ed95adea556e5cce6a1eb41f5712d43f MD5 · raw file

  1. <tool id="solid_qual_boxplot" name="Draw quality score boxplot" version="1.0.0">
  2. <description>for SOLiD data</description>
  3. <command interpreter="bash">qualsolid_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
  4. <inputs>
  5. <param format="txt" name="input" type="data" label="Statistics report file (output of 'Quality Statistics for SOLiD data' tool)" />
  6. </inputs>
  7. <outputs>
  8. <data format="png" name="output" metadata_source="input" />
  9. </outputs>
  10. <help>
  11. **What it does**
  12. Creates a boxplot graph for the quality scores in the library.
  13. .. class:: infomark
  14. **TIP:** Use the **Quality Statistics for SOLiD data** tool to generate the report file needed for this tool.
  15. -----
  16. **Output Example**
  17. * Black horizontal lines are medians
  18. * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
  19. * Whiskers show outliers at max. 1.5*IQR
  20. .. image:: ${static_path}/images/solid_qual.png
  21. ------
  22. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
  23. .. __: http://hannonlab.cshl.edu/fastx_toolkit/
  24. </help>
  25. </tool>