/tools/metag_tools/megablast_xml_parser.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 60 lines · 47 code · 13 blank · 0 comment · 0 complexity · 9832879b90a0ac447a1bfc424f1619a9 MD5 · raw file

  1. <tool id="megablast_xml_parser" name="Parse blast XML output">
  2. <description></description>
  3. <command interpreter="python">megablast_xml_parser.py $input1 $output1</command>
  4. <inputs>
  5. <param name="input1" type="data" format="blastxml" label="Megablast XML output" />
  6. </inputs>
  7. <outputs>
  8. <data name="output1" format="tabular"/>
  9. </outputs>
  10. <tests>
  11. <test>
  12. <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" />
  13. <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" />
  14. </test>
  15. </tests>
  16. <help>
  17. **What it does**
  18. This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option).
  19. -----
  20. **Output fields**
  21. This tools returns tab-delimited output with the following fields::
  22. Description Example
  23. ----------------------------------------- -----------------
  24. 1. Name of the query sequence Seq1
  25. 2. Length of the query sequence 30
  26. 3. Name of target sequence gnl|BL_ORD_ID|0
  27. 4. Length of target sequence 5528445
  28. 5. Alignment bit score 59.96
  29. 6. E-value 8.38112e-11
  30. 7. Start of alignment within query 1
  31. 8. End of alignment within query 30
  32. 9. Start of alignment within target 5436010
  33. 10. End of alignment within target 5436039
  34. 11. Query frame 1
  35. 12. Target frame 1
  36. 13. Number of identical bases within 29
  37. the alignment
  38. 14. Alignment length 30
  39. 15. Aligned portion (sequence) of query CGGACAGCGCCGCCACCAACAAAGCCACCA
  40. 16. Aligned portion (sequence) of target CGGACAGCGCCGCCACCAACAAAGCCATCA
  41. 17. Midline indicating positions of ||||||||||||||||||||||||||| ||
  42. matches within the alignment
  43. ------
  44. .. class:: infomark
  45. Note that this form of output does not contain alignment identify value. However, it can be computed by dividing the number of identical bases within the alignment (Field 13) by the alignment length (Field 14) using *Text Manipulation->Compute* tool
  46. </help>
  47. </tool>