/tools/metag_tools/blat_mapping.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 42 lines · 30 code · 12 blank · 0 comment · 0 complexity · 76e3a3f4d57a2b353f1f0a9de4597e8a MD5 · raw file

  1. <tool id="blat2wig" name="Coverage of the Reads">
  2. <description>in wiggle format</description>
  3. <command interpreter="python">blat_mapping.py $input1 $output1</command>
  4. <inputs>
  5. <param name="input1" type="data" format="tabular" label="Alignment result"/>
  6. </inputs>
  7. <outputs>
  8. <data name="output1" format="wig"/>
  9. </outputs>
  10. <tests>
  11. <test>
  12. <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" />
  13. <output name="output1" file="blat_mapping_test1.out" />
  14. </test>
  15. </tests>
  16. <help>
  17. .. class:: warningmark
  18. To generate acceptable files, please use alignment program **BLAT** with option **-out=pslx**.
  19. .. class:: warningmark
  20. Please edit the database information by click on the pencil icon next to your dataset. Select the corresponding genome build.
  21. -----
  22. **What it does**
  23. This tool takes **BLAT pslx** output and returns a wig-like file showing the number of reads (coverage) mapped at each chromosome location. Use **Graph/Display Data --> Build custom track** tool to show the coverage mapping in UCSC Genome Browser.
  24. -----
  25. **Example**
  26. Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track:
  27. .. image:: ${static_path}/images/blat_mapping_example.png
  28. :width: 600
  29. </help>
  30. </tool>