/tools/fastx_toolkit/fastq_quality_boxplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 56 lines · 31 code · 24 blank · 1 comment · 0 complexity · 36c57bd2fe0070bcb56d95be99a5a596 MD5 · raw file

  1. <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
  2. <description></description>
  3. <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
  4. <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
  5. <inputs>
  6. <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
  7. </inputs>
  8. <outputs>
  9. <data format="png" name="output" metadata_source="input" />
  10. </outputs>
  11. <help>
  12. **What it does**
  13. Creates a boxplot graph for the quality scores in the library.
  14. .. class:: infomark
  15. **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
  16. -----
  17. **Output Examples**
  18. * Black horizontal lines are medians
  19. * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
  20. * Whiskers show outlier at max. 1.5*IQR
  21. An excellent quality library (median quality is 40 for almost all 36 cycles):
  22. .. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png
  23. A relatively good quality library (median quality degrades towards later cycles):
  24. .. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png
  25. A low quality library (median drops quickly):
  26. .. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png
  27. ------
  28. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
  29. .. __: http://hannonlab.cshl.edu/fastx_toolkit/
  30. </help>
  31. </tool>
  32. <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->